@article {pmid31704413,
year = {2020},
author = {Rehman, ZU and Fortunato, L and Cheng, T and Leiknes, T},
title = {Metagenomic analysis of sludge and early-stage biofilm communities of a submerged membrane bioreactor.},
journal = {The Science of the total environment},
volume = {701},
number = {},
pages = {134682},
doi = {10.1016/j.scitotenv.2019.134682},
pmid = {31704413},
issn = {1879-1026},
mesh = {*Biofilms ; Biofouling ; Bioreactors/*microbiology ; Membranes, Artificial ; Metagenome ; *Microbiota ; Sewage/microbiology ; *Waste Disposal, Fluid ; },
abstract = {Biofilm formation on membranes in activated sludge membrane bioreactors (MBR), commonly identified as biofouling, is a significant problem for MBR operations. A better understanding of microbial species involved in the biofilm formation is needed to develop anti-biofilm measures. A read-based and genome-resolved shotgun metagenomic approach was applied to characterize the composition and functional potential of the sludge and early stage biofilm microbial communities in an MBR process. Read-based analysis revealed that the prevalence of different phyla are relatively similar in both the sludge and biofilm samples, with Proteobacteria as the most dominant, followed by Chloroflexi, Bacteroidetes and Planctomycetes. However, the relative abundance of these phyla slightly varies between the sludge and biofilm. Phyla such as Actinobacteria, bacterial candidate phyla, Chlamydiae, Cyanobacteria/Melainabacteria and Firmicutes are 2 to 4 times more abundant in the biofilm than in the sludge. At the genus level, genera belonging to Proteobacteria (Legionella, Caulobacter, Sphingomonas, Acinetobacter and Rhizobium), Cyanobacteria (Hassallia), and Spirochaetes (Turneriella) are at least twice more abundant in the biofilm. These genera, especially those belonging to Phylum Proteobacteria, are known to play an important role in the formation of biofilms on surfaces. The Alpha diversity is found slightly higher in the biofilm, compared with sludge samples. Functional classification of reads through the SEED subsystem shows that functional classes such as those involved in the metabolism of various molecules are significantly different in the biofilm and sludge. A phylogenomic analysis of the six extracted metagenome assembled genomes (MAGs) shows that three MAGs belong to Proteobacteria, and one MAG belong to each of Chloroflexi, Bacteroidetes and Planctomycetes. The relative abundance of the MAG belonging to Alphaproteobacteria is higher in the biofilm. A functional potential analysis of the MAGs reveals their potential to metabolize carbon and nitrogen sources, as well as the prevalence of antibiotic resistance genes.},
}

*Biofilms
Biofouling
Bioreactors/*microbiology
Membranes, Artificial
Metagenome
*Microbiota
Sewage/microbiology
*Waste Disposal, Fluid

@article {pmid31248008,
year = {2019},
author = {Steury, RA and Currey, MC and Cresko, WA and Bohannan, BJM},
title = {Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback.},
journal = {Genes},
volume = {10},
number = {7},
pages = {},
doi = {10.3390/genes10070484},
pmid = {31248008},
issn = {2073-4425},
support = {P50GM098911/NH/NIH HHS/United States ; R24RR032670/NH/NIH HHS/United States ; },
mesh = {Animals ; Environment ; Gastrointestinal Microbiome/*genetics ; *Genetic Variation ; Genetics, Population ; Geography ; Host Microbial Interactions ; Metagenomics ; Microbiota ; Oregon ; Smegmamorpha/genetics/*microbiology ; },
abstract = {Much of animal-associated microbiome research has been conducted in species for which little is known of their natural ecology and evolution. Microbiome studies that combine population genetic, environment, and geographic data for wild organisms can be very informative, especially in situations where host genetic variation and the environment both influence microbiome variation. The few studies that have related population genetic and microbiome variation in wild populations have been constrained by observation-based kinship data or incomplete genomic information. Here we integrate population genomic and microbiome analyses in wild threespine stickleback fish distributed throughout western Oregon, USA. We found that gut microbiome diversity and composition partitioned more among than within wild host populations and was better explained by host population genetic divergence than by environment and geography. We also identified gut microbial taxa that were most differentially abundant across environments and across genetically divergent populations. Our findings highlight the benefits of studies that investigate host-associated microbiomes in wild organisms.},
}

Animals
Environment
Gastrointestinal Microbiome/*genetics
*Genetic Variation
Genetics, Population
Geography
Host Microbial Interactions
Metagenomics
Microbiota
Oregon
Smegmamorpha/genetics/*microbiology

@article {pmid31164469,
year = {2019},
author = {Namasivayam, S and Kauffman, KD and McCulloch, JA and Yuan, W and Thovarai, V and Mittereder, LR and Trinchieri, G and Barber, DL and Sher, A},
title = {Correlation between Disease Severity and the Intestinal Microbiome in Mycobacterium tuberculosis-Infected Rhesus Macaques.},
journal = {mBio},
volume = {10},
number = {3},
pages = {},
doi = {10.1128/mBio.01018-19},
pmid = {31164469},
issn = {2150-7511},
mesh = {Animals ; Disease Susceptibility/*microbiology ; Dysbiosis/microbiology ; Female ; *Gastrointestinal Microbiome ; Macaca mulatta/microbiology ; Male ; Metagenomics ; Mycobacterium tuberculosis/pathogenicity ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Tuberculosis/*microbiology ; },
abstract = {The factors that determine host susceptibility to tuberculosis (TB) are poorly defined. The microbiota has been identified as a key influence on the nutritional, metabolic, and immunological status of the host, although its role in the pathogenesis of TB is currently unclear. Here, we investigated the influence of Mycobacterium tuberculosis exposure on the microbiome and conversely the impact of the intestinal microbiome on the outcome of M. tuberculosis exposure in a rhesus macaque model of tuberculosis. Animals were infected with different strains and doses of M. tuberculosis in three independent experiments, resulting in a range of disease severities. The compositions of the microbiotas were then assessed using a combination of 16S rRNA and metagenomic sequencing in fecal samples collected pre- and postinfection. Clustering analyses of the microbiota compositions revealed that alterations in the microbiome after M. tuberculosis infection were of much lower magnitude than the variability seen between individual monkeys. However, the microbiomes of macaques that developed severe disease were noticeably distinct from those of the animals with less severe disease as well as from each other. In particular, the bacterial families Lachnospiraceae and Clostridiaceae were enriched in monkeys that were more susceptible to infection, while numbers of Streptococcaceae were decreased. These findings in infected nonhuman primates reveal that certain baseline microbiome communities may strongly associate with the development of severe tuberculosis following infection and can be more important disease correlates than alterations to the microbiota following M. tuberculosis infection itself.IMPORTANCE Why some but not all individuals infected with Mycobacterium tuberculosis develop disease is poorly understood. Previous studies have revealed an important influence of the microbiota on host resistance to infection with a number of different disease agents. Here, we investigated the possible role of the individual's microbiome in impacting the outcome of M. tuberculosis infection in rhesus monkeys experimentally exposed to this important human pathogen. Although M. tuberculosis infection itself caused only minor alterations in the composition of the gut microbiota in these animals, we observed a significant correlation between an individual monkey's microbiome and the severity of pulmonary disease. More importantly, this correlation between microbiota structure and disease outcome was evident even prior to infection. Taken together, our findings suggest that the composition of the microbiome may be a useful predictor of tuberculosis progression in infected individuals either directly because of the microbiome's direct influence on host resistance or indirectly because of its association with other host factors that have this influence. This calls for exploration of the potential of the microbiota composition as a predictive biomarker through carefully designed prospective studies.},
}

Animals
Disease Susceptibility/*microbiology
Dysbiosis/microbiology
Female
*Gastrointestinal Microbiome
Macaca mulatta/microbiology
Male
Metagenomics
Mycobacterium tuberculosis/pathogenicity
Prospective Studies
RNA, Ribosomal, 16S/genetics
Tuberculosis/*microbiology

@article {pmid30788772,
year = {2019},
author = {Federici, M},
title = {Gut microbiome and microbial metabolites: a new system affecting metabolic disorders.},
journal = {Journal of endocrinological investigation},
volume = {42},
number = {9},
pages = {1011-1018},
doi = {10.1007/s40618-019-01022-9},
pmid = {30788772},
issn = {1720-8386},
mesh = {*Gastrointestinal Microbiome ; Humans ; Metabolic Diseases/*etiology/metabolism/pathology ; *Metabolome ; },
abstract = {INTRODUCTION: The gut microbiome is emerging as an important player in the field of metabolic disorders.

MATERIALS AND METHODS: Currently, several studies are ongoing to determine whether the effect of gut microbiome on obesity, type 2 diabetes, non-alcoholic fatty liver disease, and other metabolic diseases is determined by singular species or rather by a functional role of bacterial metabolism at higher taxonomical level. Deciphering if a single or more species are responsible for metabolic traits or rather microbial metabolic pathways are responsible for effects on host metabolism may help to identify appropriate dietary interventions to support microbial functions according to the prevalent host disease. Furthermore, the combination of metagenomics and metabolomics-based signature might be applied in the future to improve the risk prediction in healthy subjects.

CONCLUSION: In this review, I will summarize the current findings regarding the role of gut microbiome and metabolites in metabolic disorders to argue whether the current achievements may be translated into clinical practice.},
}

*Gastrointestinal Microbiome
Humans
Metabolic Diseases/*etiology/metabolism/pathology
*Metabolome

@article {pmid30282116,
year = {2019},
author = {Taylor, SL and O'Farrell, HE and Simpson, JL and Yang, IA and Rogers, GB},
title = {The contribution of respiratory microbiome analysis to a treatable traits model of care.},
journal = {Respirology (Carlton, Vic.)},
volume = {24},
number = {1},
pages = {19-28},
doi = {10.1111/resp.13411},
pmid = {30282116},
issn = {1440-1843},
mesh = {Airway Management/*methods ; Humans ; Metagenomics/methods ; Microbiological Phenomena ; *Microbiota/drug effects/physiology ; Models, Organizational ; Patient Care Management/*organization & administration ; *Pulmonary Disease, Chronic Obstructive/immunology/microbiology/physiopathology/therapy ; Respiratory System/*microbiology ; },
abstract = {The composition of the airway microbiome in patients with chronic airway diseases, such as severe asthma, chronic obstructive pulmonary disease (COPD), bronchiectasis and cystic fibrosis (CF), has the potential to inform a precision model of clinical care. Patients with these conditions share overlapping disease characteristics, including airway inflammation and airflow limitation. The clinical management of chronic respiratory conditions is increasingly moving away from a one-size-fits-all model based on primary diagnosis, towards care targeting individual disease traits, and is particularly useful for subgroups of patients who respond poorly to conventional therapies. Respiratory microbiome analysis is an important potential contributor to such a 'treatable traits' approach, providing insight into both microbial drivers of airways disease, and the selective characteristics of the changing lower airway environment. We explore the potential to integrate respiratory microbiome analysis into a treatable traits model of clinical care and provide a practical guide to the application and clinical interpretation of respiratory microbiome analysis.},
}

Airway Management/*methods
Humans
Metagenomics/methods
Microbiological Phenomena
*Microbiota/drug effects/physiology
Models, Organizational
Patient Care Management/*organization & administration
*Pulmonary Disease, Chronic Obstructive/immunology/microbiology/physiopathology/therapy
Respiratory System/*microbiology

@article {pmid31965701,
year = {2020},
author = {Muñoz-Arenas, LC and Fusaro, C and Hernández-Guzmán, M and Dendooven, L and Estrada-Torres, A and Navarro-Noya, YE},
title = {Soil microbial diversity drops with land use change in a high mountain temperate forest: a metagenomics survey.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.12822},
pmid = {31965701},
issn = {1758-2229},
abstract = {Land-use change has been identified as the most severe threat to biodiversity. Soils are important biodiversity reservoirs, but to what extent conversion of high altitude temperate forest to arable land affects taxonomic and functional soil biodiversity is still largely unknown. Shotgun metagenomics was used to determine the taxonomic and functional diversity of Bacteria, Archaea and DNA Virus in terms of effective number of species in high altitude temperate Oak and Pine-oak forest and arable soils from Mexico. Generally, the soil ecosystem maintained its microbial species richness notwithstanding land-use change. Archaea diversity was not affected by land-use change, but the bacterial diversity decreased with 45-55% when the oak forest was converted to arable land and 65-75% when the pine-oak forest was. Loss in bacterial diversity as a result of land-use change was positively correlated (R2 = 0.41) with the 10 to 25% loss in functional diversity. The archaeal communities were evener than the bacterial ones, which might explain their different response to land-use change. We expected a decrease in DNA viral communities as the bacterial diversity decreased, i.e. their potential hosts. However, a higher viral diversity was found in the arable than in the forest soils. It was found that converting high altitude oak and pine-oak forests to arable land more than halved the bacterial diversity, but did not affect the archaeal and even increased the viral diversity. This article is protected by copyright. All rights reserved.},
}

@article {pmid31824656,
year = {2019},
author = {Barton, W and O'Sullivan, O and Cotter, PD},
title = {Metabolic phenotyping of the human microbiome.},
journal = {F1000Research},
volume = {8},
number = {},
pages = {},
pmid = {31824656},
issn = {2046-1402},
mesh = {Humans ; Metabolomics ; *Microbiota ; },
abstract = {The human microbiome has been identified as having a key role in health and numerous diseases. Trillions of microbial cells and viral particles comprise the microbiome, each representing modifiable working elements of an intricate bioactive ecosystem. The significance of the human microbiome as it relates to human biology has progressed through culture-dependent (for example, media-based methods) and, more recently, molecular (for example, genetic sequencing and metabolomic analysis) techniques. The latter have become increasingly popular and evolved from being used for taxonomic identification of microbiota to elucidation of functional capacity (sequencing) and metabolic activity (metabolomics). This review summarises key elements of the human microbiome and its metabolic capabilities within the context of health and disease.},
}

Humans
Metabolomics
*Microbiota

@article {pmid31629904,
year = {2019},
author = {Almeida, AR and Alves, M and Domingues, I and Henriques, I},
title = {The impact of antibiotic exposure in water and zebrafish gut microbiomes: A 16S rRNA gene-based metagenomic analysis.},
journal = {Ecotoxicology and environmental safety},
volume = {186},
number = {},
pages = {109771},
doi = {10.1016/j.ecoenv.2019.109771},
pmid = {31629904},
issn = {1090-2414},
mesh = {Animals ; Anti-Bacterial Agents/*toxicity ; Aquaculture ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Metagenome/*drug effects/genetics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/*toxicity ; Zebrafish/genetics/*microbiology ; },
abstract = {In order to supply human demand for food, the aquaculture industry has been growing fast in the last years, being fish usually cultivated in overcrowded conditions. Hence, to prevent the rapidly disease spreading, antibiotics may be applied to both sick and healthy animals. Due to its broad spectrum, oxytetracycline (OTC) is one of the most used antibiotics in food-production. Yet, although useful to prevent infections, antibiotics may reshape aquatic animals' microbiome, disturbing hosts' welfare. However, the impact of this exposure to the organism microbiome and its surrounding environment is poorly understood. Then, the objective of this study was to analyze in detail the long-term effect of OTC in both zebrafish gut and water microbiomes. Zebrafish adults were exposed, via water, for two months to three concentrations of OTC (0, 10 and 10000 μg/L). Total DNA was extracted from gut and water samples and the V3-V4 region of the bacterial 16 S rRNA gene was sequenced using Illumina technology. Results of alpha and beta-diversity analyses revealed that long-term exposure to OTC impacted both zebrafish gut and water microbiomes. In water samples, effects were observed even at the lowest (10 μg/L) OTC concentration tested resulting in an increase in Deltaproteobacteria, namely the Myxococcales and Bdellovibrionales orders. On the other hand, effects on zebrafish gut were only observed at the highest concentration with the selection of Alphaproteobacteria and Actinobacteria classes. Although these classes are common in fish gut, the increase of Actinobacteria may represent a health problem since some genera like Gordonia are linked to some human infection disease. Nevertheless, in both gut and water, it was observed a decrease in Gamaproteobacteria, probably due to OTC mode of action. In silico functional metagenomic analysis revealed that OTC exposure selected general detoxification mechanisms. In addition, the abundance of functional genes involved in Quorum Sensing (QS) increased under OTC exposure suggesting that QS may help bacteria to survive OTC stress. Thus, future studies should consider post-exposure scenarios for a deeper analysis of the water and zebrafish gut resistome, since bacteria may react differently after exposure ceased.},
}

Animals
Anti-Bacterial Agents/*toxicity
Aquaculture
Gastrointestinal Microbiome/*drug effects/genetics
Humans
Metagenome/*drug effects/genetics
Metagenomics
RNA, Ribosomal, 16S/genetics
Water Pollutants, Chemical/*toxicity
Zebrafish/genetics/*microbiology

@article {pmid31454888,
year = {2019},
author = {Borghi, E and Vignoli, A},
title = {Rett Syndrome and Other Neurodevelopmental Disorders Share Common Changes in Gut Microbial Community: A Descriptive Review.},
journal = {International journal of molecular sciences},
volume = {20},
number = {17},
pages = {},
doi = {10.3390/ijms20174160},
pmid = {31454888},
issn = {1422-0067},
mesh = {Animals ; Biodiversity ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Neurodevelopmental Disorders/diagnosis/*etiology ; Phenotype ; Rett Syndrome/diagnosis/*etiology ; },
abstract = {In this narrative review, we summarize recent pieces of evidence of the role of microbiota alterations in Rett syndrome (RTT). Neurological problems are prominent features of the syndrome, but the pathogenic mechanisms modulating its severity are still poorly understood. Gut microbiota was recently demonstrated to be altered both in animal models and humans with different neurodevelopmental disorders and/or epilepsy. By investigating gut microbiota in RTT cohorts, a less rich microbial community was identified which was associated with alterations of fecal microbial short-chain fatty acids. These changes were positively correlated with severe clinical outcomes. Indeed, microbial metabolites can play a crucial role both locally and systemically, having dynamic effects on host metabolism and gene expression in many organs. Similar alterations were found in patients with autism and down syndrome as well, suggesting a potential common pathway of gut microbiota involvement in neurodevelopmental disorders.},
}

Animals
Biodiversity
Dysbiosis
*Gastrointestinal Microbiome
Humans
Metagenome
Metagenomics/methods
Neurodevelopmental Disorders/diagnosis/*etiology
Phenotype
Rett Syndrome/diagnosis/*etiology

@article {pmid31450659,
year = {2019},
author = {Aarnoutse, R and Ziemons, J and Penders, J and Rensen, SS and de Vos-Geelen, J and Smidt, ML},
title = {The Clinical Link between Human Intestinal Microbiota and Systemic Cancer Therapy.},
journal = {International journal of molecular sciences},
volume = {20},
number = {17},
pages = {},
doi = {10.3390/ijms20174145},
pmid = {31450659},
issn = {1422-0067},
mesh = {Combined Modality Therapy/adverse effects/methods ; Disease Management ; *Gastrointestinal Microbiome/drug effects/radiation effects ; Humans ; Metagenome ; Metagenomics/methods ; Neoplasms/complications/mortality/*therapy ; Prognosis ; Treatment Outcome ; },
abstract = {Clinical interest in the human intestinal microbiota has increased considerably. However, an overview of clinical studies investigating the link between the human intestinal microbiota and systemic cancer therapy is lacking. This systematic review summarizes all clinical studies describing the association between baseline intestinal microbiota and systemic cancer therapy outcome as well as therapy-related changes in intestinal microbiota composition. A systematic literature search was performed and provided 23 articles. There were strong indications for a close association between the intestinal microbiota and outcome of immunotherapy. Furthermore, the development of chemotherapy-induced infectious complications seemed to be associated with the baseline microbiota profile. Both chemotherapy and immunotherapy induced drastic changes in gut microbiota composition with possible consequences for treatment efficacy. Evidence in the field of hormonal therapy was very limited. Large heterogeneity concerning study design, study population, and methods used for analysis limited comparability and generalization of results. For the future, longitudinal studies investigating the predictive ability of baseline intestinal microbiota concerning treatment outcome and complications as well as the potential use of microbiota-modulating strategies in cancer patients are required. More knowledge in this field is likely to be of clinical benefit since modulation of the microbiota might support cancer therapy in the future.},
}

Combined Modality Therapy/adverse effects/methods
Disease Management
*Gastrointestinal Microbiome/drug effects/radiation effects
Humans
Metagenome
Metagenomics/methods
Neoplasms/complications/mortality/*therapy
Prognosis
Treatment Outcome

@article {pmid31119104,
year = {2019},
author = {Govender, Y and Gabriel, I and Minassian, V and Fichorova, R},
title = {The Current Evidence on the Association Between the Urinary Microbiome and Urinary Incontinence in Women.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {133},
doi = {10.3389/fcimb.2019.00133},
pmid = {31119104},
issn = {2235-2988},
mesh = {Female ; *Host Microbial Interactions ; Humans ; *Microbiota ; Prevalence ; Risk Factors ; Urinary Incontinence/*epidemiology/*physiopathology ; Urinary Tract/*microbiology ; },
abstract = {Urinary incontinence (UI) is a burdensome condition with high prevalence in middle-aged to older women and an unclear etiology. Advances in our understanding of host-microbe interactions in the urogenital tract have stimulated interest in the urinary microbiome. DNA sequencing and enhanced urine culture suggest that similarly to other mucosal sites, the urinary bladder of healthy individuals harbors resident microbial communities that may play distinct roles in bladder function. This review focused on the urobiome (expanded quantitative urine culture-based or genomic sequencing-based urinary microbiome) associated with different subtypes of UI, including stress, urgency and mixed urinary incontinence, and related syndromes, such as interstitial cystitis and overactive bladder in women, contrasted to urinary tract infections. Furthermore, we examined clinical evidence for the association of the urinary microbiome with responses to pharmacotherapy for amelioration of UI symptoms. Although published studies are still relatively limited in number, study design and sample size, cumulative evidence suggests that certain Lactobacillus species may play a role in maintaining a healthy bladder milieu. Higher bacterial diversity in the absence of Lactobacillus dominance was associated with urgency UI and resistance to anticholinergic treatment for this condition. UI may also facilitate the persistence of uropathogens following antibiotic treatment, which in turn can alter the commensal/potentially beneficial microbial communities. Risk factors of UI, including age, menopausal status, sex steroid hormones, and body mass index may also impact the urinary microbiome. However, it is yet unclear whether the effects of these risks factors on UI are mediated by urinary host-microbe interactions and a mechanistic link with the female urogenital microbiome is still to be established. Strategies for future research are suggested.},
}

Female
*Host Microbial Interactions
Humans
*Microbiota
Prevalence
Risk Factors
Urinary Incontinence/*epidemiology/*physiopathology
Urinary Tract/*microbiology

@article {pmid31053982,
year = {2019},
author = {Van Dexter, S and Oubre, C and Boopathy, R},
title = {Carbon ecology of termite gut and phenol degradation by a bacterium isolated from the gut of termite.},
journal = {Journal of industrial microbiology & biotechnology},
volume = {46},
number = {9-10},
pages = {1265-1271},
pmid = {31053982},
issn = {1476-5535},
mesh = {Animals ; Bacteria/isolation & purification/*metabolism ; Carbon/*metabolism ; Cellobiose/metabolism ; Ecosystem ; Gastrointestinal Microbiome ; Isoptera/*microbiology ; Metagenomics ; Phenols/*metabolism ; },
abstract = {Metagenomics and transcriptomics have had some success analyzing community and functional ecology of the termite gut, but carbon utilization ecology and the effect of diet on the gut community are not well understood. This study was done to determine the effect of three hardwood tree types, oak (Quercus spp.), red maple (Acer rubrum), and tupelo (Nyssa aquatica) on the termite species, Reticulitermes flavipes in the family Rhinotermitidae. Termite abdomen homogenates were incubated on agar plates containing three common carbon sources in the termite gut, namely, acetate, cellobiose, and phenol under aerobic and anaerobic conditions. Bacterial growth was higher on cellobiose than any other carbon source. Higher bacterial growth on cellobiose was observed from termite colonies feeding on oak than on phenol from the other two wood types. The difference between aerobic and anaerobic conditions was not significant. A bacterium, Acinetobacter tandoii isolated and identified from our previous study was subjected to high concentrations of phenol as the sole carbon source and this bacterium was able to degrade phenol concentration up to 600 mg/L.},
}

Animals
Bacteria/isolation & purification/*metabolism
Carbon/*metabolism
Cellobiose/metabolism
Ecosystem
Gastrointestinal Microbiome
Isoptera/*microbiology
Metagenomics
Phenols/*metabolism

@article {pmid31521989,
year = {2019},
author = {Breton-Deval, L and Sanchez-Flores, A and Juárez, K and Vera-Estrella, R},
title = {Integrative study of microbial community dynamics and water quality along The Apatlaco River.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {255},
number = {Pt 1},
pages = {113158},
doi = {10.1016/j.envpol.2019.113158},
pmid = {31521989},
issn = {1873-6424},
mesh = {Bacteria/classification/*isolation & purification ; Biological Oxygen Demand Analysis ; Environmental Monitoring/*methods ; Humans ; Mexico ; Microbiota ; Nitrogen/analysis ; Oxygen/analysis ; Phosphorus/analysis ; Rivers/chemistry/*microbiology ; Urbanization ; Water Pollutants, Chemical/*analysis ; Water Pollution/*analysis ; Water Quality ; },
abstract = {The increasing demand for clean water resources for human consumption, is raising concerning about the sustainable worldwide provisioning. In Mexico, rivers near to high-density urbanizations are subject to irrational exploitation where polluted water is a risk for human health. Therefore, the aims of this study are to analyze water quality parameters and bacterial community dynamics to understand the relation between them, in the Apatlaco river, which presents a clear environmental perturbance. Parameters such as total coliforms, chemical oxygen demand, harness, ammonium, nitrite, nitrate, total Kjeldahl nitrogen, dissolved oxygen, total phosphorus, total dissolved solids, and temperature were analyzed in 17 sampling points along the river. The high pollution level was registered in the sampling point 10 with 480 mg/L chemical oxygen demand, 7 mg/L nitrite, 34 mg/L nitrate, 2 mg/L dissolved oxygen, and 299 mg/L of total dissolved solids. From these sites, we selected four samples for DNA extraction and performed a metagenomic analysis using a whole metagenome shotgun approach, to compare the microbial communities between polluted and non-polluted sites. In general, Proteobacteria was the most representative phylum in all sites. However, the clean water reference point was enriched with microorganism from the Limnohabitans genus, a planktonic bacterium widespread in freshwater ecosystems. Nevertheless, in the polluted sampled sites, we found a high abundance of potential opportunistic pathogen genera such as Acinetobacter, Arcobacter, and Myroides, among others. This suggests that in addition to water contamination, an imminent human health risk due to pathogenic bacteria can potentially affect a population of ∼1.6 million people dwelling nearby. These results will contribute to the knowledge regarding anthropogenic pollution on the microbial population dynamic and how they affect human health and life quality.},
}

Bacteria/classification/*isolation & purification
Biological Oxygen Demand Analysis
Environmental Monitoring/*methods
Humans
Mexico
Microbiota
Nitrogen/analysis
Oxygen/analysis
Phosphorus/analysis
Rivers/chemistry/*microbiology
Urbanization
Water Pollutants, Chemical/*analysis
Water Pollution/*analysis
Water Quality

@article {pmid31110364,
year = {2019},
author = {Diamond, S and Andeer, PF and Li, Z and Crits-Christoph, A and Burstein, D and Anantharaman, K and Lane, KR and Thomas, BC and Pan, C and Northen, TR and Banfield, JF},
title = {Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms.},
journal = {Nature microbiology},
volume = {4},
number = {8},
pages = {1356-1367},
pmid = {31110364},
issn = {2058-5276},
mesh = {Bacteria/classification/*genetics/metabolism ; Biodiversity ; California ; Carbon/*metabolism ; Carbon Cycle ; Ecology ; Ecosystem ; *Genomics ; *Grassland ; Metagenomics ; Nitrogen/*metabolism ; Nitrogen Cycle ; Proteomics ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C1 metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C1, nitrate and ammonia transformations, and constrain factors that impact their distributions in soil.},
}

Bacteria/classification/*genetics/metabolism
Biodiversity
California
Carbon/*metabolism
Carbon Cycle
Ecology
Ecosystem
*Genomics
*Grassland
Metagenomics
Nitrogen/*metabolism
Nitrogen Cycle
Proteomics
Soil/*chemistry
*Soil Microbiology

@article {pmid31055031,
year = {2019},
author = {Seferovic, MD and Pace, RM and Carroll, M and Belfort, B and Major, AM and Chu, DM and Racusin, DA and Castro, ECC and Muldrew, KL and Versalovic, J and Aagaard, KM},
title = {Visualization of microbes by 16S in situ hybridization in term and preterm placentas without intraamniotic infection.},
journal = {American journal of obstetrics and gynecology},
volume = {221},
number = {2},
pages = {146.e1-146.e23},
doi = {10.1016/j.ajog.2019.04.036},
pmid = {31055031},
issn = {1097-6868},
mesh = {Adult ; DNA Barcoding, Taxonomic ; Female ; Humans ; In Situ Hybridization ; Metagenomics ; Microbiota ; Placenta/*microbiology ; Pregnancy ; Premature Birth ; RNA, Bacterial/analysis ; *RNA, Ribosomal, 16S ; Sequence Analysis, RNA ; Term Birth ; },
abstract = {BACKGROUND: Numerous reports have documented bacteria in the placental membranes and basal plate decidua in the absence of immunopathology using histologic techniques. Similarly, independent metagenomic characterizations have identified an altered taxonomic makeup in association with spontaneous preterm birth. Here we sought to corroborate these findings by localizing presumptive intact bacteria using molecular histology within the placental microanatomy.

OBJECTIVE: Here we examined for microbes in term and preterm gestations using a signal-amplified 16S universal in situ hybridization probe set for bacterial rRNA, alongside traditional histologic methods of Warthin-Starry and Gram stains, as well as clinical culture methodologies. We further sought to differentiate accompanying 16S gene sequencing taxonomic profiles from germ-free (gnotobiotic) mouse and extraction and amplicon contamination controls.

STUDY DESIGN: Placentas were collected from a total of 53 subjects, composed of term labored (n = 4) and unlabored cesarean deliveries (n = 22) and preterm vaginal (n = 18) and cesarean deliveries (n = 8); a placenta from a single subject with clinical and histologic evident choriomanionitis was employed as a positive control (n = 1). The preterm cohort included spontaneous preterm birth with (n = 6) and without (n = 10) preterm premature rupture of membranes, as well as medically indicated preterm births (n = 10). Placental microbes were visualized using an in situ hybridization probe set designed against highly conserved regions of the bacterial 16S ribosome, which produces an amplified stable signal using branched DNA probes. Extracted bacterial nucleic acids from these same samples were subjected to 16S rRNA metagenomic sequencing (Illumina, V4) for course taxonomic analysis, alongside environmental and kit contaminant controls. A subset of unlabored, cesarean-delivered term pregnancies were also assessed with clinical culture for readily cultivatable pathogenic microbes.

RESULTS: Molecular in situ hybridization of bacterial rRNA enabled visualization and localization of low-abundance microbes after systematic high-power scanning. Despite the absence of clinical or histologic chorioamnionitis in 52 of 53 subjects, instances of 16S rRNA signal were confidently observed in 13 of 16 spontaneous preterm birth placentas, which was not significantly different from term unlabored cesarean specimens (18 of 22; P > .05). 16S rRNA signal was largely localized to the villous parenchyma and/or syncytiotrophoblast, and less commonly the chorion and the maternal intervillous space. In all term and unlabored cesarean deliveries, visualization of evident placental microbes by in situ hybridization occurred in the absence of clinical or histologic detection using conventional clinical cultivation, hematoxylin-eosin, and Gram staining. In 1 subject, appreciable villous bacteria localized to an infarction, where 16S microbial detection was confirmed by Warthin-Starry stain. In all instances, parallel sample principle coordinate analysis using Bray-Cutis distances of 16S rRNA gene sequencing data demonstrated consistent taxonomic distinction from all negative or potential contamination controls (P = .024, PERMANOVA). Classification from contaminant filtered data identified a distinct taxonomic makeup among term and preterm cohorts when compared with contaminant controls (false discovery rate <0.05).

CONCLUSION: Presumptively intact placental microbes are visualized as low-abundance, low-biomass and sparse populations within the placenta regardless of gestational age and mode of delivery. Their taxonomic makeup is distinct from contamination controls. These findings further support several previously published findings, including our own, which have used metagenomics to characterize low-abundance and low-biomass microbial communities in the placenta.},
}

Adult
DNA Barcoding, Taxonomic
Female
Humans
In Situ Hybridization
Metagenomics
Microbiota
Placenta/*microbiology
Pregnancy
Premature Birth
RNA, Bacterial/analysis
*RNA, Ribosomal, 16S
Sequence Analysis, RNA
Term Birth

@article {pmid31289831,
year = {2019},
author = {Youens-Clark, K and Bomhoff, M and Ponsero, AJ and Wood-Charlson, EM and Lynch, J and Choi, I and Hartman, JH and Hurwitz, BL},
title = {iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences.},
journal = {GigaScience},
volume = {8},
number = {7},
pages = {},
doi = {10.1093/gigascience/giz083},
pmid = {31289831},
issn = {2047-217X},
mesh = {Big Data ; Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; *Software ; },
abstract = {BACKGROUND: Scientists have amassed a wealth of microbiome datasets, making it possible to study microbes in biotic and abiotic systems on a population or planetary scale; however, this potential has not been fully realized given that the tools, datasets, and computation are available in diverse repositories and locations. To address this challenge, we developed iMicrobe.us, a community-driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with those from the broader community.

FINDINGS: The iMicrobe platform brings together analysis tools and microbiome datasets by leveraging National Science Foundation-supported cyberinfrastructure and computing resources from CyVerse, Agave, and XSEDE. The primary purpose of iMicrobe is to provide users with a freely available, web-based platform to (1) maintain and share project data, metadata, and analysis products, (2) search for related public datasets, and (3) use and publish bioinformatics tools that run on highly scalable computing resources. Analysis tools are implemented in containers that encapsulate complex software dependencies and run on freely available XSEDE resources via the Agave API, which can retrieve datasets from the CyVerse Data Store or any web-accessible location (e.g., FTP, HTTP).

CONCLUSIONS: iMicrobe promotes data integration, sharing, and community-driven tool development by making open source data and tools accessible to the research community in a web-based platform.},
}

Big Data
Metagenome
Metagenomics/*methods
Microbiota/*genetics
*Software

@article {pmid31232514,
year = {2019},
author = {Matesanz, S and Pescador, DS and Pías, B and Sánchez, AM and Chacón-Labella, J and Illuminati, A and de la Cruz, M and López-Angulo, J and Marí-Mena, N and Vizcaíno, A and Escudero, A},
title = {Estimating belowground plant abundance with DNA metabarcoding.},
journal = {Molecular ecology resources},
volume = {19},
number = {5},
pages = {1265-1277},
doi = {10.1111/1755-0998.13049},
pmid = {31232514},
issn = {1755-0998},
support = {CGL2015-66809-P//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; },
mesh = {*Biota ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Metagenomics/*methods ; Plant Roots/classification/genetics ; Plants/*classification/*genetics ; },
abstract = {Most work on plant community ecology has been performed above ground, neglecting the processes that occur in the soil. DNA metabarcoding, in which multiple species are computationally identified in bulk samples, can help to overcome the logistical limitations involved in sampling plant communities belowground. However, a major limitation of this methodology is the quantification of species' abundances based on the percentage of sequences assigned to each taxon. Using root tissues of five dominant species in a semi-arid Mediterranean shrubland (Bupleurum fruticescens, Helianthemum cinereum, Linum suffruticosum, Stipa pennata and Thymus vulgaris), we built pairwise mixtures of relative abundance (20%, 50% and 80% biomass), and implemented two methods (linear model fits and correction indices) to improve estimates of root biomass. We validated both methods with multispecies mixtures that simulate field-collected samples. For all species, we found a positive and highly significant relationship between the percentage of sequences and biomass in the mixtures (R2 = .44-.66), but the equations for each species (slope and intercept) differed among them, and two species were consistently over- and under-estimated. The correction indices greatly improved the estimates of biomass percentage for all five species in the multispecies mixtures, and reduced the overall error from 17% to 6%. Our results show that, through the use of post-sequencing quantification methods on mock communities, DNA metabarcoding can be effectively used to determine not only species' presence but also their relative abundance in field samples of root mixtures. Importantly, knowledge of these aspects will allow us to study key, yet poorly understood, belowground processes.},
}

*Biota
DNA Barcoding, Taxonomic/*methods
DNA, Plant/genetics
Metagenomics/*methods
Plant Roots/classification/genetics
Plants/*classification/*genetics

@article {pmid31353293,
year = {2019},
author = {Powell, EA and Fontanella, S and Boakes, E and Belgrave, D and Shaw, AG and Cornwell, E and Fernandez-Crespo, R and Fink, CG and Custovic, A and Kroll, JS},
title = {Temporal association of the development of oropharyngeal microbiota with early life wheeze in a population-based birth cohort.},
journal = {EBioMedicine},
volume = {46},
number = {},
pages = {486-498},
doi = {10.1016/j.ebiom.2019.07.034},
pmid = {31353293},
issn = {2352-3964},
mesh = {Age Factors ; Biodiversity ; Cohort Studies ; Female ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Oropharynx/*microbiology ; Population Surveillance ; Respiratory Sounds/*etiology ; United Kingdom/epidemiology ; },
abstract = {BACKGROUND: A critical window in infancy has been proposed, during which the microbiota may affect subsequent health. The longitudinal development of the oropharyngeal microbiota is under-studied and may be associated with early-life wheeze. We aimed to investigate the temporal association of the development of the oropharyngeal microbiota with early-life wheeze.

METHODS: A population-based birth cohort based in London, UK was followed for 24 months. We collected oropharyngeal swabs at six time-points. Microbiota was determined using sequencing of the V3-V5 region of the 16S rRNA-encoding gene. Medical records were reviewed for the outcome of doctor diagnosed wheeze. We used a time-varying model to investigate the temporal association between the development of microbiota and doctor-diagnosed wheeze.

FINDINGS: 159 participants completed the study to 24 months and for 98 there was complete sequencing data at all timepoints and outcome data. Of these, 26 had doctor-diagnosed wheeze. We observed significant increase in the abundance of Neisseria between 9 and 24 months in children who developed wheeze (p = 0∙003), while in those without wheezing there was a significant increment in the abundance of Granulicatella (p = 0∙012) between 9 and 12 months, and of Prevotella (p = 0∙018) after 18 months.

INTERPRETATION: A temporal association between the respiratory commensal Granulicatella and also Prevotella with wheeze (negative), and between Neisseria and wheeze (positive) was identified in infants prior to one year of age. This adds to evidence for the proposed role of the microbiota in the development of wheeze. FUND: Research funding from the Winnicott Foundation, Meningitis Now and Micropathology Ltd.},
}

Age Factors
Biodiversity
Cohort Studies
Female
Humans
Male
Metagenome
Metagenomics/methods
*Microbiota
Oropharynx/*microbiology
Population Surveillance
Respiratory Sounds/*etiology
United Kingdom/epidemiology

@article {pmid31327695,
year = {2019},
author = {Clos-Garcia, M and Andrés-Marin, N and Fernández-Eulate, G and Abecia, L and Lavín, JL and van Liempd, S and Cabrera, D and Royo, F and Valero, A and Errazquin, N and Vega, MCG and Govillard, L and Tackett, MR and Tejada, G and Gónzalez, E and Anguita, J and Bujanda, L and Orcasitas, AMC and Aransay, AM and Maíz, O and López de Munain, A and Falcón-Pérez, JM},
title = {Gut microbiome and serum metabolome analyses identify molecular biomarkers and altered glutamate metabolism in fibromyalgia.},
journal = {EBioMedicine},
volume = {46},
number = {},
pages = {499-511},
doi = {10.1016/j.ebiom.2019.07.031},
pmid = {31327695},
issn = {2352-3964},
mesh = {Adult ; Aged ; Biomarkers ; Chromatography, High Pressure Liquid ; Computational Biology/methods ; Cytokines/metabolism ; Female ; Fibromyalgia/*etiology/*metabolism ; *Gastrointestinal Microbiome ; Glutamates/*metabolism ; Humans ; Male ; *Metabolome ; *Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; ROC Curve ; Tandem Mass Spectrometry ; },
abstract = {BACKGROUND: Fibromyalgia is a complex, relatively unknown disease characterised by chronic, widespread musculoskeletal pain. The gut-brain axis connects the gut microbiome with the brain through the enteric nervous system (ENS); its disruption has been associated with psychiatric and gastrointestinal disorders. To gain an insight into the pathogenesis of fibromyalgia and identify diagnostic biomarkers, we combined different omics techniques to analyse microbiome and serum composition.

METHODS: We collected faeces and blood samples to study the microbiome, the serum metabolome and circulating cytokines and miRNAs from a cohort of 105 fibromyalgia patients and 54 age- and environment-matched healthy individuals. We sequenced the V3 and V4 regions of the 16S rDNA gene from faeces samples. UPLC-MS metabolomics and custom multiplex cytokine and miRNA analysis (FirePlex™ technology) were used to examine sera samples. Finally, we combined the different data types to search for potential biomarkers.

RESULTS: We found that the diversity of bacteria is reduced in fibromyalgia patients. The abundance of the Bifidobacterium and Eubacterium genera (bacteria participating in the metabolism of neurotransmitters in the host) in these patients was significantly reduced. The serum metabolome analysis revealed altered levels of glutamate and serine, suggesting changes in neurotransmitter metabolism. The combined serum metabolomics and gut microbiome datasets showed a certain degree of correlation, reflecting the effect of the microbiome on metabolic activity. We also examined the microbiome and serum metabolites, cytokines and miRNAs as potential sources of molecular biomarkers of fibromyalgia.

CONCLUSIONS: Our results show that the microbiome analysis provides more significant biomarkers than the other techniques employed in the work. Gut microbiome analysis combined with serum metabolomics can shed new light onto the pathogenesis of fibromyalgia. We provide a list of bacteria whose abundance changes in this disease and propose several molecules as potential biomarkers that can be used to evaluate the current diagnostic criteria.},
}

Adult
Aged
Biomarkers
Chromatography, High Pressure Liquid
Computational Biology/methods
Cytokines/metabolism
Female
Fibromyalgia/*etiology/*metabolism
*Gastrointestinal Microbiome
Glutamates/*metabolism
Humans
Male
*Metabolome
*Metabolomics/methods
Metagenome
Metagenomics/methods
Middle Aged
RNA, Ribosomal, 16S/genetics
ROC Curve
Tandem Mass Spectrometry

@article {pmid31021803,
year = {2019},
author = {Wassan, JT and Wang, H and Browne, F and Zheng, H},
title = {Phy-PMRFI: Phylogeny-Aware Prediction of Metagenomic Functions Using Random Forest Feature Importance.},
journal = {IEEE transactions on nanobioscience},
volume = {18},
number = {3},
pages = {273-282},
doi = {10.1109/TNB.2019.2912824},
pmid = {31021803},
issn = {1558-2639},
mesh = {Algorithms ; Databases, Genetic ; *Decision Trees ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*genetics ; *Metagenomics/classification/methods ; Microbiota/genetics ; Pharynx/microbiology ; Phylogeny ; *Support Vector Machine ; },
abstract = {High-throughput sequencing techniques have accelerated functional metagenomics studies through the generation of large volumes of omics data. The integration of these data using computational approaches is potentially useful for predicting metagenomic functions. Machine learning (ML) models can be trained using microbial features which are then used to classify microbial data into different functional classes. For example, ML analyses over the human microbiome data has been linked to the prediction of important biological states. For analysing omics data, integrating abundance count of taxonomical features with their biological relationships is important. These relationships can potentially be uncovered from the phylogenetic tree of microbial taxa. In this paper, we propose a novel integrative framework Phy-PMRFI. This framework is driven by the phylogeny-based modeling of omics data to predict metagenomic functions using important features selected by a random forest importance (RFI) strategy. The proposed framework integrates the underlying phylogenetic tree information with abundance measures of microbial species (features) by creating a novel phylogeny and abundance aware matrix structure (PAAM). Phy-PMRFI progresses by ranking the microbial features using an RFI measure. This is then used as input for microbiome classification. The resultant feature set enhances the performance of the state-of-art methods such as support vector machines. Our proposed integrative framework also outperforms the state-of-the-art pipeline of phylogenetic isometric log-ratio transform (PhILR) and MetaPhyl. Prediction accuracy of 90 % is obtained with Phy-PMRFI over human throat microbiome in comparison to other approaches of PhILR with 53% and MetaPhyl with 71% accuracy.},
}

Algorithms
Databases, Genetic
*Decision Trees
High-Throughput Nucleotide Sequencing
Humans
Metagenome/*genetics
*Metagenomics/classification/methods
Microbiota/genetics
Pharynx/microbiology
Phylogeny
*Support Vector Machine

@article {pmid30853704,
year = {2019},
author = {Watahiki, S and Kimura, N and Yamazoe, A and Miura, T and Sekiguchi, Y and Noda, N and Matsukura, S and Kasai, D and Takahata, Y and Nojiri, H and Fukuda, M},
title = {Ecological impact assessment of a bioaugmentation site on remediation of chlorinated ethylenes by multi-omics analysis.},
journal = {The Journal of general and applied microbiology},
volume = {65},
number = {5},
pages = {225-233},
doi = {10.2323/jgam.2018.10.003},
pmid = {30853704},
issn = {1349-8037},
abstract = {Bioremediation may affect the ecological system around bioremediation sites. However, little is known about how microbial community structures change over time after the initial injection of degraders. In this study, we have assessed the ecological impact of bioaugmentation using metagenomic and metatranscriptomic approaches to remove trichlorinated ethylene/cis-dichloroethylene (TCE/cDCE) by Rhodococcus jostii strain RHA1 as an aerobic chemical compound degrader. Metagenomic analysis showed that the number of organisms belonging to the genus Rhodococcus, including strain RHA1, increased from 0.1% to 76.6% of the total microbial community on day 0 at the injection site. Subsequently, the populations of strain RHA1 and other TCE/cDCE-degrading bacteria gradually decreased over time, whereas the populations of the anaerobic dechlorinators Geobacter and Dehalococcoides increased at later stages. Metatranscriptomic analysis revealed a high expression of aromatic compound-degrading genes (bphA1-A4) in strain RHA1 after RHA1 injection. From these results, we concluded that the key dechlorinators of TCE/cDCE were mainly aerobic bacteria, such as RHA1, until day 1, after which the key dechlorinators changed to anaerobic bacteria, such as Geobacter and Dehalococcocides, after day 6 at the injection well. Based on the α-diversity, the richness levels of the microbial community were increased after injection of strain RHA1, and the microbial community composition had not been restored to that of the original composition during the 19 days after treatment. These results provide insights into the assessment of the ecological impact and bioaugmentation process of RHA1 at bioremediation sites.},
}

@article {pmid30809227,
year = {2019},
author = {Schwarzer, M and Hermanova, P and Srutkova, D and Golias, J and Hudcovic, T and Zwicker, C and Sinkora, M and Akgün, J and Wiedermann, U and Tuckova, L and Kozakova, H and Schabussova, I},
title = {Germ-Free Mice Exhibit Mast Cells With Impaired Functionality and Gut Homing and Do Not Develop Food Allergy.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {205},
doi = {10.3389/fimmu.2019.00205},
pmid = {30809227},
issn = {1664-3224},
abstract = {Background: Mucosal mast cells (MC) are key players in IgE-mediated food allergy (FA). The evidence on the interaction between gut microbiota, MC and susceptibility to FA is contradictory. Objective: We tested the hypothesis that commensal bacteria are essential for MC migration to the gut and their maturation impacting the susceptibility to FA. Methods: The development and severity of FA symptoms was studied in sensitized germ-free (GF), conventional (CV), and mice mono-colonized with L. plantarum WCFS1 or co-housed with CV mice. MC were phenotypically and functionally characterized. Results: Systemic sensitization and oral challenge of GF mice with ovalbumin led to increased levels of specific IgE in serum compared to CV mice. Remarkably, despite the high levels of sensitization, GF mice did not develop diarrhea or anaphylactic hypothermia, common symptoms of FA. In the gut, GF mice expressed low levels of the MC tissue-homing markers CXCL1 and CXCL2, and harbored fewer MC which exhibited lower levels of MC protease-1 after challenge. Additionally, MC in GF mice were less mature as confirmed by flow-cytometry and their functionality was impaired as shown by reduced edema formation after injection of degranulation-provoking compound 48/80. Co-housing of GF mice with CV mice fully restored their susceptibility to develop FA. However, this did not occur when mice were mono-colonized with L. plantarum. Conclusion: Our results demonstrate that microbiota-induced maturation and gut-homing of MC is a critical step for the development of symptoms of experimental FA. This new mechanistic insight into microbiota-MC-FA axis can be exploited in the prevention and treatment of FA in humans.},
}

@article {pmid31267543,
year = {2020},
author = {Zhang, L and Li, YY and Tang, X and Zhao, X},
title = {Faecal microbial dysbiosis in children with Wiskott-Aldrich syndrome.},
journal = {Scandinavian journal of immunology},
volume = {91},
number = {1},
pages = {e12805},
doi = {10.1111/sji.12805},
pmid = {31267543},
issn = {1365-3083},
mesh = {Animals ; Biodiversity ; Biomarkers ; Case-Control Studies ; Child, Preschool ; Disease Models, Animal ; *Dysbiosis ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Inflammatory Bowel Diseases/etiology ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Mice, Knockout ; Mutation ; RNA, Ribosomal, 16S/genetics ; Wiskott-Aldrich Syndrome/diagnosis/*etiology ; Wiskott-Aldrich Syndrome Protein/deficiency ; },
abstract = {Wiskott-Aldrich syndrome (WAS) is an X-linked primary immunodeficiency disease caused by a mutation in the WAS gene that encodes the WAS protein (WASp); up to 5-10% of these patients develop inflammatory bowel disease (IBD). The mechanisms by which WASp deficiency causes IBD are unclear. Intestinal microbial dysbiosis and imbalances in host immune responses play important roles in the pathogenesis of polygenetic IBD; however, few studies have conducted detailed examination of the microbial alterations and their relationship with IBD in WAS. Here, we collected faecal samples from 19 children (all less than 2 years old) with WAS and samples from WASp-KO mice with IBD and subjected them to 16S ribosomal RNA sequencing. We found that microbial community richness and structure in WAS children were different from those in controls; WAS children revealed reduced microbial community richness and diversity. Relative abundance of Bacteroidetes and Verrucomicrobiain in WAS children was significantly lower, while that of Proteobacteria was markedly higher. WASp-KO mice revealed a significantly decreased abundance of Firmicutes. Faecal microbial dysbiosis caused by WASp deficiency is similar to that observed for polygenetic IBD, suggesting that WASp may play crucial function in microbial homoeostasis and that microbial dysbiosis may contribute to IBD in WAS. These microbial alterations may be useful targets for monitoring and therapeutically managing intestinal inflammation in WAS.},
}

Animals
Biodiversity
Biomarkers
Case-Control Studies
Child, Preschool
Disease Models, Animal
*Dysbiosis
Feces/*microbiology
Female
*Gastrointestinal Microbiome
Humans
Infant
Inflammatory Bowel Diseases/etiology
Male
Metagenome
Metagenomics/methods
Mice
Mice, Knockout
Mutation
RNA, Ribosomal, 16S/genetics
Wiskott-Aldrich Syndrome/diagnosis/*etiology
Wiskott-Aldrich Syndrome Protein/deficiency

@article {pmid31083685,
year = {2019},
author = {Grant, ET and Kyes, RC and Kyes, P and Trinh, P and Ramirez, V and Tanee, T and Pinlaor, P and Dangtakot, R and Rabinowitz, PM},
title = {Fecal microbiota dysbiosis in macaques and humans within a shared environment.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0210679},
doi = {10.1371/journal.pone.0210679},
pmid = {31083685},
issn = {1932-6203},
support = {P51 OD010425/OD/NIH HHS/United States ; T42 OH008433/OH/NIOSH CDC HHS/United States ; },
mesh = {Animals ; Biodiversity ; Cross-Sectional Studies ; *Environment ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Macaca fascicularis ; Metagenome ; Metagenomics/methods ; Thailand ; },
abstract = {Traditional zoonotic disease research focuses on detection of recognized pathogens and may miss opportunities to understand broader microbial transmission dynamics between humans, animals, and the environment. We studied human-macaque microbiome overlap in Kosum Phisai District, Maha Sarakham Province, Thailand, where a growing population of long-tailed macaques (Macaca fascicularis) in Kosumpee Forest Park interact with humans from an adjacent village. We surveyed workers in or near the park with elevated exposure to macaques to characterize tasks resulting in exposure to macaque feces in addition to dietary and lifestyle factors that influence gut microbiome composition. Fecal samples were collected from 12 exposed workers and 6 controls without macaque exposure, as well as 8 macaques from Kosumpee Forest Park and 4 from an isolated forest patch with minimal human contact. The V4 region of the 16S rRNA gene from fecal sample extracted DNA was amplified and sequenced using Illumina MiSeq to characterize the microbial community. A permuted betadisper test on the weighted UniFrac distances revealed significant differences in the dispersion patterns of gut microbiota from exposed and control macaques (p = 0.03). The high variance in gut microbiota composition of macaques in contact with humans has potential implications for gut microbiome stability and susceptibility to disease, described by the Anna Karenina principle (AKP). Human samples had homogenous variance in beta diversity but different spatial medians between groups (p = 0.02), indicating a shift in microbial composition that may be explained by fundamental lifestyle differences between the groups unrelated to exposure status. SourceTracker was used to estimate the percent of gut taxa in exposed humans that was contributed by macaques. While one worker showed evidence of elevated contribution, the overall trend was not significant. Task observations among workers revealed opportunities to employ protective measures or training to reduce exposure to occupational hazards. These results suggest the potential for hygiene measures to mitigate negative aspects of contact between humans and macaques in order to optimize the health of both populations.},
}

Animals
Biodiversity
Cross-Sectional Studies
*Environment
Feces/*microbiology
*Gastrointestinal Microbiome
Humans
Macaca fascicularis
Metagenome
Metagenomics/methods
Thailand

@article {pmid31562300,
year = {2019},
author = {Liu, J and Taft, DH and Maldonado-Gomez, MX and Johnson, D and Treiber, ML and Lemay, DG and DePeters, EJ and Mills, DA},
title = {The fecal resistome of dairy cattle is associated with diet during nursing.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4406},
doi = {10.1038/s41467-019-12111-x},
pmid = {31562300},
issn = {2041-1723},
support = {R01 AT007079/AT/NCCIH NIH HHS/United States ; R01 AT008759/AT/NCCIH NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; },
mesh = {Animal Feed/*analysis ; Animals ; Animals, Newborn ; Anti-Bacterial Agents/pharmacology ; Cattle ; Colostrum/microbiology ; Dairying ; *Diet ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/drug effects/genetics ; *Gene Regulatory Networks ; Genes, Bacterial/*genetics ; Manure/microbiology ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; },
abstract = {Antimicrobial resistance is a global public health concern, and livestock play a significant role in selecting for resistance and maintaining such reservoirs. Here we study the succession of dairy cattle resistome during early life using metagenomic sequencing, as well as the relationship between resistome, gut microbiota, and diet. In our dataset, the gut of dairy calves serves as a reservoir of 329 antimicrobial resistance genes (ARGs) presumably conferring resistance to 17 classes of antibiotics, and the abundance of ARGs declines gradually during nursing. ARGs appear to co-occur with antibacterial biocide or metal resistance genes. Colostrum is a potential source of ARGs observed in calves at day 2. The dynamic changes in the resistome are likely a result of gut microbiota assembly, which is closely associated with diet transition in dairy calves. Modifications in the resistome may be possible via early-life dietary interventions to reduce overall antimicrobial resistance.},
}

Animal Feed/*analysis
Animals
Animals, Newborn
Anti-Bacterial Agents/pharmacology
Cattle
Colostrum/microbiology
Dairying
*Diet
Drug Resistance, Multiple, Bacterial/drug effects/*genetics
Feces/*microbiology
Gastrointestinal Microbiome/drug effects/genetics
*Gene Regulatory Networks
Genes, Bacterial/*genetics
Manure/microbiology
Metagenomics/methods
RNA, Ribosomal, 16S/genetics
Soil Microbiology

@article {pmid31554820,
year = {2019},
author = {Riva, A and Kuzyk, O and Forsberg, E and Siuzdak, G and Pfann, C and Herbold, C and Daims, H and Loy, A and Warth, B and Berry, D},
title = {A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4366},
doi = {10.1038/s41467-019-12413-0},
pmid = {31554820},
issn = {2041-1723},
mesh = {Animals ; Colon/*microbiology ; *Diet ; Dietary Fiber/*deficiency ; Gastrointestinal Microbiome/genetics/*physiology ; Intestinal Mucosa/microbiology ; Metagenomics/methods ; Mice, Inbred C57BL ; Microbiota/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Compartmentalization of the gut microbiota is thought to be important to system function, but the extent of spatial organization in the gut ecosystem remains poorly understood. Here, we profile the murine colonic microbiota along longitudinal and lateral axes using laser capture microdissection. We found fine-scale spatial structuring of the microbiota marked by gradients in composition and diversity along the length of the colon. Privation of fiber reduces the diversity of the microbiota and disrupts longitudinal and lateral gradients in microbiota composition. Both mucus-adjacent and luminal communities are influenced by the absence of dietary fiber, with the loss of a characteristic distal colon microbiota and a reduction in the mucosa-adjacent community, concomitant with depletion of the mucus layer. These results indicate that diet has not only global but also local effects on the composition of the gut microbiota, which may affect function and resilience differently depending on location.},
}

Animals
Colon/*microbiology
*Diet
Dietary Fiber/*deficiency
Gastrointestinal Microbiome/genetics/*physiology
Intestinal Mucosa/microbiology
Metagenomics/methods
Mice, Inbred C57BL
Microbiota/genetics/*physiology
RNA, Ribosomal, 16S/genetics

@article {pmid31437154,
year = {2019},
author = {Pichler, V and Kotsakiozi, P and Caputo, B and Serini, P and Caccone, A and Della Torre, A},
title = {Complex interplay of evolutionary forces shaping population genomic structure of invasive Aedes albopictus in southern Europe.},
journal = {PLoS neglected tropical diseases},
volume = {13},
number = {8},
pages = {e0007554},
doi = {10.1371/journal.pntd.0007554},
pmid = {31437154},
issn = {1935-2735},
support = {R01 AI132409/AI/NIAID NIH HHS/United States ; },
mesh = {Aedes/classification/*genetics ; Albania ; Animal Migration ; Animals ; *Biological Evolution ; Europe ; Gene Flow ; Genetic Variation ; Greece ; Insect Vectors/classification/*genetics ; Introduced Species ; Italy ; *Metagenomics ; Phylogeny ; Polymorphism, Single Nucleotide ; },
abstract = {BACKGROUND: In the last four decades, the Asian tiger mosquito, Aedes albopictus, vector of several human arboviruses, has spread from its native range in South-East Asia to all over the world, largely through the transportation of its eggs via the international trade in used tires. Albania was the first country invaded in Europe in 1979, followed by Italy in 1990 and other Mediterranean countries after 2000.

METHODS/PRINCIPAL FINDINGS: We here inferred the invasion history and migration patterns of Ae. albopictus in Italy (today the most heavily-infested country in Europe), Greece and Albania, by analyzing a panel of >100,000 single nucleotide polymorphisms (SNPs) obtained by sequencing of double-digest Restriction site-Associated DNA (ddRADseq). The obtained dataset was combined with samples previously analyzed from both the native and invasive range worldwide to interpret the results using a broader spatial and historical context. The emerging evolutionary scenario complements the results of other studies in showing that the extraordinary worldwide expansion of Ae. albopictus has occurred thanks to multiple independent invasions by large numbers of colonists from multiple geographic locations in both native and previously invaded areas, consistently with the role of used tires shipments to move large numbers of eggs worldwide. By analyzing mosquitoes from nine sites across ~1,000-km transect in Italy, we were able to detect a complex interplay of drift, isolation by distance mediated divergence, and gene flow in shaping the species very recent invasion and range expansion, suggesting overall high connectivity, likely due to passive transportation of adults via ground transportation, as well as specific adaptations to local conditions.

CONCLUSIONS/SIGNIFICANCE: Results contribute to characterize one of the most successful histories of animal invasion, and could be used as a baseline for future studies to track epidemiologically relevant characters (e.g. insecticide resistance).},
}

Aedes/classification/*genetics
Albania
Animal Migration
Animals
*Biological Evolution
Europe
Gene Flow
Genetic Variation
Greece
Insect Vectors/classification/*genetics
Introduced Species
Italy
*Metagenomics
Phylogeny
Polymorphism, Single Nucleotide

@article {pmid31926407,
year = {2019},
author = {Edge, TA and Baird, DJ and Bilodeau, G and Gagné, N and Greer, C and Konkin, D and Newton, G and Séguin, A and Beaudette, L and Bilkhu, S and Bush, A and Chen, W and Comte, J and Condie, J and Crevecoeur, S and El-Kayssi, N and Emilson, EJS and Fancy, DL and Kandalaft, I and Khan, IUH and King, I and Kreutzweiser, D and Lapen, D and Lawrence, J and Lowe, C and Lung, O and Martineau, C and Meier, M and Ogden, N and Paré, D and Phillips, L and Porter, TM and Sachs, J and Staley, Z and Steeves, R and Venier, L and Veres, T and Watson, C and Watson, S and Macklin, J},
title = {The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada.},
journal = {The Science of the total environment},
volume = {710},
number = {},
pages = {135906},
doi = {10.1016/j.scitotenv.2019.135906},
pmid = {31926407},
issn = {1879-1026},
abstract = {Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as diverse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate biodiversity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate sampling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive biodiversity reference points to assess environmental change.},
}

@article {pmid31757198,
year = {2019},
author = {Qian, J and Comin, M},
title = {MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage.},
journal = {BMC bioinformatics},
volume = {20},
number = {Suppl 9},
pages = {367},
pmid = {31757198},
issn = {1471-2105},
mesh = {*Algorithms ; Cluster Analysis ; *Contig Mapping ; Databases, Genetic ; *Metagenome ; *Metagenomics ; Microbiota/genetics ; *Probability ; *Statistics as Topic ; },
abstract = {MOTIVATION: Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Because assembly typically produces only genome fragments, also known as contigs, it is crucial to group them into putative species for further taxonomic profiling and down-streaming functional analysis. Taxonomic analysis of microbial communities requires contig clustering, a process referred to as binning, that is still one of the most challenging tasks when analyzing metagenomic data. The major problems are the lack of taxonomically related genomes in existing reference databases, the uneven abundance ratio of species, sequencing errors, and the limitations due to binning contig of different lengths.

RESULTS: In this context we present MetaCon a novel tool for unsupervised metagenomic contig binning based on probabilistic k-mers statistics and coverage. MetaCon uses a signature based on k-mers statistics that accounts for the different probability of appearance of a k-mer in different species, also contigs of different length are clustered in two separate phases. The effectiveness of MetaCon is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, MaxBin and MetaBAT.},
}

*Algorithms
Cluster Analysis
*Contig Mapping
Databases, Genetic
*Metagenome
*Metagenomics
Microbiota/genetics
*Probability
*Statistics as Topic

@article {pmid31524629,
year = {2020},
author = {Lo, KH and Lu, CW and Lin, WH and Chien, CC and Chen, SC and Kao, CM},
title = {Enhanced reductive dechlorination of trichloroethene with immobilized Clostridium butyricum in silica gel.},
journal = {Chemosphere},
volume = {238},
number = {},
pages = {124596},
doi = {10.1016/j.chemosphere.2019.124596},
pmid = {31524629},
issn = {1879-1298},
mesh = {Biodegradation, Environmental ; Chloroflexi/growth & development/*metabolism ; Clostridium butyricum/*metabolism ; Groundwater/*chemistry ; Halogenation ; Metagenomics ; Microbiota/physiology ; Silica Gel ; Trichloroethylene/*metabolism ; },
abstract = {Deteriorated environmental conditions during the bioremediation of trichloroethene (TCE)-polluted groundwater cause decreased treatment efficiencies. This study assessed the effect of applying immobilized Clostridium butyricum (a hydrogen-producing bacterium) in silica gel on enhancing the reductive dechlorination efficiency of TCE with the slow polycolloid-releasing substrate (SPRS) supplement in groundwater. The responses of microbial communities with the immobilized system (immobilized Clostridium butyricum and SPRS amendments) were also characterized by the metagenomics assay. A complete TCE removal in microcosms was obtained within 30 days with the application of this immobilized system via reductive dechlorination processes. An increase in the population of Dehalococcoides spp. was observed using the quantitative polymerase chain reaction (qPCR) analysis. Results of metagenomics assay reveal that the microbial communities in the immobilized system were distinct from those in systems with SPRS only. Bacterial communities associated with TCE biodegradation also increased in microcosms treated with the immobilized system. The immobilized system shows a great potential to promote the TCE dechlorination efficiency, and the metagenomics-based approach provides detailed insights into dechlorinating microbial community dynamics. The results would be helpful in designing an in situ immobilized system to enhance the bioremediation efficiency of TCE-contaminated groundwater.},
}

Biodegradation, Environmental
Chloroflexi/growth & development/*metabolism
Clostridium butyricum/*metabolism
Groundwater/*chemistry
Halogenation
Metagenomics
Microbiota/physiology
Silica Gel
Trichloroethylene/*metabolism

@article {pmid31500705,
year = {2020},
author = {Dugat-Bony, E and Lossouarn, J and De Paepe, M and Sarthou, AS and Fedala, Y and Petit, MA and Chaillou, S},
title = {Viral metagenomic analysis of the cheese surface: A comparative study of rapid procedures for extracting viral particles.},
journal = {Food microbiology},
volume = {85},
number = {},
pages = {103278},
doi = {10.1016/j.fm.2019.103278},
pmid = {31500705},
issn = {1095-9998},
mesh = {Bacteriophages/genetics ; Cheese/*virology ; *Metagenome ; Metagenomics/*methods ; Microbiota ; Virion/*genetics ; Virology/methods ; },
abstract = {The structure and functioning of microbial communities from fermented foods, including cheese, have been extensively studied during the past decade. However, there is still a lack of information about both the occurrence and the role of viruses in modulating the function of this type of spatially structured and solid ecosystems. Viral metagenomics was recently applied to a wide variety of environmental samples and standardized procedures for recovering viral particles from different type of materials has emerged. In this study, we adapted a procedure originally developed to extract viruses from fecal samples, in order to enable efficient virome analysis of cheese surface. We tested and validated the positive impact of both addition of a filtration step prior to virus concentration and substitution of purification by density gradient ultracentrifugation by a simple chloroform treatment to eliminate membrane vesicles. Viral DNA extracted from the several procedures, as well as a vesicle sample, were sequenced using Illumina paired-end MiSeq technology and the subsequent clusters assembled from the virome were analyzed to assess those belonging to putative phages, plasmid-derived DNA, or even from bacterial chromosomal DNA. The best procedure was then chosen, and used to describe the first cheese surface virome, using Epoisses cheese as example. This study provides the basis of future investigations regarding the ecological importance of viruses in cheese microbial ecosystems.},
}

Bacteriophages/genetics
Cheese/*virology
*Metagenome
Metagenomics/*methods
Microbiota
Virion/*genetics
Virology/methods

@article {pmid31500701,
year = {2020},
author = {Li, Z and Dong, L and Zhao, C and Zhu, Y},
title = {Metagenomic insights into the changes in microbial community and antimicrobial resistance genes associated with different salt content of red pepper (Capsicum annuum L.) sauce.},
journal = {Food microbiology},
volume = {85},
number = {},
pages = {103295},
doi = {10.1016/j.fm.2019.103295},
pmid = {31500701},
issn = {1095-9998},
mesh = {Capsicum/*chemistry ; Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/*genetics/growth & development ; Fermentation ; Genes, Bacterial ; Lactobacillaceae/*genetics/growth & development ; *Metagenome ; Metagenomics ; *Microbiota ; Osmotic Pressure ; Sodium Chloride/*chemistry ; },
abstract = {Fermented red pepper (FRP) sauce has been eaten in worldwide for many years. The salt content and resident microbial community influences the quality of the FRP sauce and may confer health (e.g., probiotics) or harm (e.g., antibiotic resistance genes) to the consumers in some circumstances; however, the salt-mediated alteration of microbial community and antibiotic resistance genes are little known. In this study, a combination of whole genome sequencing and amplicon analysis was used to investigate the changes in microbial community and antimicrobial resistance genes in response to different salt content during red pepper fermentation. While the family Enterobacteriaceae dominated in high-salt (15-25%) samples, Lactobacillaceae quickly became the dominant population in place of Enterobacteriaceae after 24 days in 10% salt samples. Compared to 0.05 antibiotic resistance genes (ARGs) per cell number on average in 10% salt sample, 16.6 ARGs were present in high-salt samples, wherein the bacterial hosts were major assigned to Enterobacteriaceae including genera Enterobacter, Citrobacter, Escherichia, Salmonella and Klebsiella. Multidrug resistance genes were the predominant ARG type. Functional profiling showed that histidine kinase functions were of much higher abundance in high-salt samples and included several osmotic stress-related two-component systems that simultaneously encoded ARGs. These results give first metagenomic insights into the salt-mediated changes in microbial community composition and a broad view of associated antibiotic resistance genes in the process of food fermentation.},
}

Capsicum/*chemistry
Drug Resistance, Bacterial/*genetics
Enterobacteriaceae/*genetics/growth & development
Fermentation
Genes, Bacterial
Lactobacillaceae/*genetics/growth & development
*Metagenome
Metagenomics
*Microbiota
Osmotic Pressure
Sodium Chloride/*chemistry

@article {pmid31366182,
year = {2019},
author = {Deshpande, SV and Reed, TM and Sullivan, RF and Kerkhof, LJ and Beigel, KM and Wade, MM},
title = {Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS).},
journal = {Genes},
volume = {10},
number = {8},
pages = {},
doi = {10.3390/genes10080578},
pmid = {31366182},
issn = {2073-4425},
mesh = {DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome ; Metagenomics/*methods ; Microbiota ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {Field laboratories interested in using the MinION often need the internet to perform sample analysis. Thus, the lack of internet connectivity in resource-limited or remote locations renders downstream analysis problematic, resulting in a lack of sample identification in the field. Due to this dependency, field samples are generally transported back to the lab for analysis where internet availability for downstream analysis is available. These logistics problems and the time lost in sample characterization and identification, pose a significant problem for field scientists. To address this limitation, we have developed a stand-alone data analysis packet using open source tools developed by the Nanopore community that does not depend on internet availability. Like Oxford Nanopore Technologies' (ONT) cloud-based What's In My Pot (WIMP) software, we developed the offline MinION Detection Software (MINDS) based on the Centrifuge classification engine for rapid species identification. Several online bioinformatics applications have been developed surrounding ONT's framework for analysis of long reads. We have developed and evaluated an offline real time classification application pipeline using open source tools developed by the Nanopore community that does not depend on internet availability. Our application has been tested on ATCC's 20 strain even mix whole cell (ATCC MSA-2002) sample. Using the Rapid Sequencing Kit (SQK-RAD004), we were able to identify all 20 organisms at species level. The analysis was performed in 15 min using a Dell Precision 7720 laptop. Our offline downstream bioinformatics application provides a cost-effective option as well as quick turn-around time when analyzing samples in the field, thus enabling researchers to fully utilize ONT's MinION portability, ease-of-use, and identification capability in remote locations.},
}

DNA Barcoding, Taxonomic/methods
High-Throughput Nucleotide Sequencing/*methods
Metagenome
Metagenomics/*methods
Microbiota
Sequence Analysis, DNA/*methods
*Software

@article {pmid31278679,
year = {2019},
author = {Mitra, S},
title = {Multiple Data Analyses and Statistical Approaches for Analyzing Data from Metagenomic Studies and Clinical Trials.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1910},
number = {},
pages = {605-634},
doi = {10.1007/978-1-4939-9074-0_20},
pmid = {31278679},
issn = {1940-6029},
mesh = {Algorithms ; Biodiversity ; *Computational Biology/methods ; Data Interpretation, Statistical ; *Data Mining/methods ; Evolution, Molecular ; Fatty Acids, Omega-3/pharmacology ; Gastrointestinal Microbiome/drug effects ; Humans ; *Metagenome ; *Metagenomics/methods ; Microbiota ; Molecular Sequence Annotation ; Plaque, Atherosclerotic/etiology ; Workflow ; },
abstract = {Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms (microbes) obtained from a common habitat. Metagenomics and other "omics" disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. There are plenty of studies using metagenomics which examine microorganisms that inhabit niches in the human body, sometimes causing disease, and are often correlated with multiple treatment conditions. No matter from which environment it comes, the analyses are often aimed at determining either the presence or absence of specific species of interest in a given metagenome or comparing the biological diversity and the functional activity of a wider range of microorganisms within their communities. The importance increases for comparison within different environments such as multiple patients with different conditions, multiple drugs, and multiple time points of same treatment or same patient. Thus, no matter how many hypotheses we have, we need a good understanding of genomics, bioinformatics, and statistics to work together to analyze and interpret these datasets in a meaningful way. This chapter provides an overview of different data analyses and statistical approaches (with example scenarios) to analyze metagenomics samples from different medical projects or clinical trials.},
}

Algorithms
Biodiversity
*Computational Biology/methods
Data Interpretation, Statistical
*Data Mining/methods
Evolution, Molecular
Fatty Acids, Omega-3/pharmacology
Gastrointestinal Microbiome/drug effects
Humans
*Metagenome
*Metagenomics/methods
Microbiota
Molecular Sequence Annotation
Plaque, Atherosclerotic/etiology
Workflow

@article {pmid31278668,
year = {2019},
author = {Watson, AK and Lannes, R and Pathmanathan, JS and Méheust, R and Karkar, S and Colson, P and Corel, E and Lopez, P and Bapteste, E},
title = {The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1910},
number = {},
pages = {271-308},
doi = {10.1007/978-1-4939-9074-0_9},
pmid = {31278668},
issn = {1940-6029},
mesh = {Biodiversity ; Biological Evolution ; Computational Biology/methods ; Ecosystem ; Evolution, Molecular ; Gene Ontology ; Gene Regulatory Networks ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; Microbiota ; Molecular Sequence Annotation ; Multigene Family ; },
abstract = {In the post genomic era, large and complex molecular datasets from genome and metagenome sequencing projects expand the limits of what is possible for bioinformatic analyses. Network-based methods are increasingly used to complement phylogenetic analysis in studies in molecular evolution, including comparative genomics, classification, and ecological studies. Using network methods, the vertical and horizontal relationships between all genes or genomes, whether they are from cellular chromosomes or mobile genetic elements, can be explored in a single expandable graph. In recent years, development of new methods for the construction and analysis of networks has helped to broaden the availability of these approaches from programmers to a diversity of users. This chapter introduces the different kinds of networks based on sequence similarity that are already available to tackle a wide range of biological questions, including sequence similarity networks, gene-sharing networks and bipartite graphs, and a guide for their construction and analyses.},
}

Biodiversity
Biological Evolution
Computational Biology/methods
Ecosystem
Evolution, Molecular
Gene Ontology
Gene Regulatory Networks
High-Throughput Nucleotide Sequencing
*Metagenome
*Metagenomics/methods
Microbiota
Molecular Sequence Annotation
Multigene Family

@article {pmid31154531,
year = {2019},
author = {Tutuncu, HE and Balci, N and Tuter, M and Karaguler, NG},
title = {Recombinant production and characterization of a novel esterase from a hypersaline lake, Acıgöl, by metagenomic approach.},
journal = {Extremophiles : life under extreme conditions},
volume = {23},
number = {5},
pages = {507-520},
doi = {10.1007/s00792-019-01103-w},
pmid = {31154531},
issn = {1433-4909},
mesh = {Bacterial Proteins/chemistry/*genetics/metabolism ; Enzyme Stability ; Esterases/chemistry/*genetics/metabolism ; Halomonas/enzymology/genetics ; Lakes/microbiology ; *Metagenome ; Microbiota ; Salinity ; *Salt Tolerance ; Substrate Specificity ; },
abstract = {The aim of this study was to isolate a novel esterase from a hypersaline lake by sequence-based metagenomics. The metagenomic DNA was isolated from the enriched hypersaline lake sediment. Degenerate primers targeting the conserved regions of lipolytic enzymes of halophilic microorganisms were used for polymerase chain reaction (PCR) and a whole gene was identified by genome walking. The gene was composed of 783 bp, which corresponds to 260 amino acids with a molecular weight of 28.2 kDa. The deduced amino acid sequence best matched with the esterase from Halomonas gudaonensis with an identity of 91%. Recombinantly expressed enzyme exhibited maximum activity towards pNP-hexanoate with a kcat value of 12.30 s-1. The optimum pH and temperature of the enzyme were found as 9 and 30 °C, respectively. The effects of NaCl, solvents, metal ions, detergents and enzyme inhibitors were also studied. In conclusion, a novel enzyme, named as hypersaline lake "Acıgöl" esterase (hAGEst), was identified by sequence-based metagenomics. The high expression level, the ability to maintain activity at cold temperatures and tolerance to DMSO and metal ions are the most outstanding properties of the hAGEst.},
}

Bacterial Proteins/chemistry/*genetics/metabolism
Enzyme Stability
Esterases/chemistry/*genetics/metabolism
Halomonas/enzymology/genetics
Lakes/microbiology
*Metagenome
Microbiota
Salinity
*Salt Tolerance
Substrate Specificity

@article {pmid31039168,
year = {2019},
author = {De La Torre, U and Henderson, JD and Furtado, KL and Pedroja, M and Elenamarie, O and Mora, A and Pechanec, MY and Maga, EA and Mienaltowski, MJ},
title = {Utilizing the fecal microbiota to understand foal gut transitions from birth to weaning.},
journal = {PloS one},
volume = {14},
number = {4},
pages = {e0216211},
doi = {10.1371/journal.pone.0216211},
pmid = {31039168},
issn = {1932-6203},
mesh = {Animals ; Animals, Newborn ; Bacteria/growth & development ; Biodiversity ; Feces/*microbiology ; Gastrointestinal Tract/*microbiology ; Horses/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; Principal Component Analysis ; *Weaning ; },
abstract = {A healthy gastrointestinal (GI) tract with a properly established microbiota is necessary for a foal to develop into a healthy weanling. A foal's health can be critically impacted by aberrations in the microbiome such as with diarrhea which can cause great morbidity and mortality in foals. In this study, we hypothesized that gut establishment in the foal transitioning from a diet of milk to a diet of grain, forage, and pasture would be detectable through analyses of the fecal microbiotas. Fecal samples from 37 sets of foals and mares were collected at multiple time points ranging from birth to weaning. Bacterial DNA was isolated from the samples, and the V4 domain of bacterial 16S rRNA genes were amplified via polymerase chain reaction. Next generation sequencing was then performed on the resulting amplicons, and analyses were performed to characterize the microbiome as well as the relative abundance of microbiota present. We found that bacterial population compositions followed a pattern throughout the early life of the foal in an age-dependent manner. As foals transitioned from milk consumption to a forage and grain diet, there were recognizable changes in fecal microbial compositions from initial populations predominant in the ability to metabolize milk to populations capable of utilizing fibrous plant material. We were also able to recognize differences in microbial populations amongst diarrheic foals as well as microbial population differences associated with differences in management styles between facilities. Future efforts will gauge the effects of lesser abundant bacterial populations that could also be essential to GI health, as well as to determine how associations between microbial population profiles and animal management practices can be used to inform strategies for improving upon the health and growth of horses overall.},
}

Animals
Animals, Newborn
Bacteria/growth & development
Biodiversity
Feces/*microbiology
Gastrointestinal Tract/*microbiology
Horses/*microbiology
Metagenomics
*Microbiota
Phylogeny
Principal Component Analysis
*Weaning

@article {pmid31854766,
year = {2019},
author = {Hu, WC and Zhao, C and Wang, QJ and Liu, RP and Bai, YH},
title = {[Metabolic Functional Analysis of Dominant Microbial Communities in the Rapid Sand Filters for Drinking Water].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {40},
number = {8},
pages = {3604-3611},
doi = {10.13227/j.hjkx.201901167},
pmid = {31854766},
issn = {0250-3301},
mesh = {Denitrification ; *Drinking Water ; *Microbiota ; Nitrogen ; Oxidation-Reduction ; Sand ; Water Microbiology ; *Water Purification ; },
abstract = {Rapid sand filter (RSF) is widely used in drinking water treatment plants. Rapid filtration is always considered a physicochemical process, but the effect of the microorganisms that attach to the filter media remain inadequately investigated. In order to understand the composition and functional characteristics of microbial communities in RSFs, influent water, effluent water, and filter materials from eleven RSFs in eight Chinese cities were sampled and analyzed. After filtration, dissolved organic carbon (DOC) showed a slight but significant removal due to the growth of heterotrophic microbes. The activity of ammonia-oxidizing microbes and nitrite-oxidizing microbes promoted a significant decrease in ammonia nitrogen (NH4+-N) and a significant increase in nitrate nitrogen (NO3--N) in water. No significant changes in total nitrogen (TN) were observed, indicating that denitrification and anammox were weak in the RSFs. The composition and function of the microbial communities of RSFs were assessed using metagenomic methods. Genera in the top 10% with respect to relative abundance (14 genera in total) were identified as the dominant genera, including the two ammonia-oxidizing bacteria Nitrospira and Nitrosomonas. Functional gene information for the dominant genera was also extracted for analysis. The dominant genera exhibited higher relative abundances of carbohydrate, nitrogen, sulfur, and xenobiotic metabolic pathways. Aeromonas had the highest relative abundance of carbohydrate metabolic genes, and Bradyrhizobium had the highest relative abundance of nitrogen, sulfur, and xenobiotics metabolic genes, indicating that these two genera play an important role in the transformation of substances in drinking water. Finally, the metabolic potential of the dominant genera on xenobiotics was evaluated, and the results showed that Bradyrhizobium, Sphingomonas, Methyloglobulus, Sphingopyxis, and Klebsiella were the key bacterial genera for the removal of micropollutants in RSFs.},
}

Denitrification
*Drinking Water
*Microbiota
Nitrogen
Oxidation-Reduction
Sand
Water Microbiology
*Water Purification

@article {pmid31673867,
year = {2019},
author = {Puri, RR and Adachi, F and Omichi, M and Saeki, Y and Yamamoto, A and Hayashi, S and Ali, MA and Itoh, K},
title = {Metagenomic study of endophytic bacterial community of sweet potato (Ipomoea batatas) cultivated in different soil and climatic conditions.},
journal = {World journal of microbiology & biotechnology},
volume = {35},
number = {11},
pages = {176},
pmid = {31673867},
issn = {1573-0972},
support = {16KT0032//Japan Society for the Promotion of Science/ ; },
mesh = {Bacteria/*classification/genetics/*metabolism ; Base Sequence ; Biodiversity ; *Climate ; DNA, Bacterial/analysis ; DNA, Mitochondrial/analysis ; Endophytes/*classification/genetics ; Ipomoea batatas/*microbiology ; *Metagenome ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; Soil Microbiology ; },
abstract = {The aim of this study was to clarify effects of soil and climatic conditions on community structure of sweet potato bacterial endophytes by applying locked nucleic acid oligonucleotide-PCR clamping technique and metagenomic analysis. For this purpose, the soil samples in three locations were transferred each other and sweet potato nursery plants from the same farm were cultivated for ca. 3 months. After removal of plastid, mitochondria and undefined sequences, the averaged numbers of retained sequences and operational taxonomic units per sample were 20,891 and 846, respectively. Proteobacteria (85.0%), Bacteroidetes (6.6%) and Actinobacteria (6.3%) were the three most dominant phyla, accounting for 97.9% of the reads, and γ-Proteobacteria (66.3%) being the most abundant. Top 10 genera represented 81.2% of the overall reads in which Pseudomonas (31.9-45.0%) being the most predominant. The overall endophytic bacterial communities were similar among the samples which indicated that the soil and the climatic conditions did not considerably affect the entire endophytic community. The original endophytic bacterial community might be kept during the cultivation period.},
}

Bacteria/*classification/genetics/*metabolism
Base Sequence
Biodiversity
*Climate
DNA, Bacterial/analysis
DNA, Mitochondrial/analysis
Endophytes/*classification/genetics
Ipomoea batatas/*microbiology
*Metagenome
*Microbiota/genetics
Phylogeny
RNA, Ribosomal, 16S/genetics
Soil/*chemistry
Soil Microbiology

@article {pmid31492655,
year = {2019},
author = {Soto-Perez, P and Bisanz, JE and Berry, JD and Lam, KN and Bondy-Denomy, J and Turnbaugh, PJ},
title = {CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog.},
journal = {Cell host & microbe},
volume = {26},
number = {3},
pages = {325-335.e5},
pmid = {31492655},
issn = {1934-6069},
support = {DP5 OD021344/OD/NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; },
mesh = {Actinobacteria/virology ; Bacteria/genetics/*virology ; Bacteriophages/*genetics ; Base Sequence ; *CRISPR-Cas Systems ; DNA, Bacterial/analysis ; DNA, Viral/analysis ; Databases, Genetic ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Genome, Viral ; Humans ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA ; },
abstract = {Bacteriophages are abundant within the human gastrointestinal tract, yet their interactions with gut bacteria remain poorly understood, particularly with respect to CRISPR-Cas immunity. Here, we show that the type I-C CRISPR-Cas system in the prevalent gut Actinobacterium Eggerthella lenta is transcribed and sufficient for specific targeting of foreign and chromosomal DNA. Comparative analyses of E. lenta CRISPR-Cas systems across (meta)genomes revealed 2 distinct clades according to cas sequence similarity and spacer content. We assembled a human virome database (HuVirDB), encompassing 1,831 samples enriched for viral DNA, to identify protospacers. This revealed matches for a majority of spacers, a marked increase over other databases, and uncovered "hyper-targeted" phage sequences containing multiple protospacers targeted by several E. lenta strains. Finally, we determined the positional mismatch tolerance of observed spacer-protospacer pairs. This work emphasizes the utility of merging computational and experimental approaches for determining the function and targets of CRISPR-Cas systems.},
}

Actinobacteria/virology
Bacteria/genetics/*virology
Bacteriophages/*genetics
Base Sequence
*CRISPR-Cas Systems
DNA, Bacterial/analysis
DNA, Viral/analysis
Databases, Genetic
Gastrointestinal Tract/*microbiology
Genome, Bacterial
Genome, Viral
Humans
Metagenomics
Microbiota/genetics
Sequence Analysis, DNA

@article {pmid31488812,
year = {2019},
author = {Mora, M and Wink, L and Kögler, I and Mahnert, A and Rettberg, P and Schwendner, P and Demets, R and Cockell, C and Alekhova, T and Klingl, A and Krause, R and Zolotariof, A and Alexandrova, A and Moissl-Eichinger, C},
title = {Space Station conditions are selective but do not alter microbial characteristics relevant to human health.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {3990},
doi = {10.1038/s41467-019-11682-z},
pmid = {31488812},
issn = {2041-1723},
mesh = {Archaea/*classification/genetics/isolation & purification ; Bacteria/*classification/genetics/isolation & purification ; Biodiversity ; Biofilms/growth & development ; Extremophiles ; Fungi/*classification/genetics/isolation & purification ; *Health ; Host Microbial Interactions ; Humans ; Metagenomics ; Microbiota/genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Space Flight ; },
abstract = {The International Space Station (ISS) is a unique habitat for humans and microorganisms. Here, we report the results of the ISS experiment EXTREMOPHILES, including the analysis of microbial communities from several areas aboard at three time points. We assess microbial diversity, distribution, functional capacity and resistance profile using a combination of cultivation-independent analyses (amplicon and shot-gun sequencing) and cultivation-dependent analyses (physiological and genetic characterization of microbial isolates, antibiotic resistance tests, co-incubation experiments). We show that the ISS microbial communities are highly similar to those present in ground-based confined indoor environments and are subject to fluctuations, although a core microbiome persists over time and locations. The genomic and physiological features selected by ISS conditions do not appear to be directly relevant to human health, although adaptations towards biofilm formation and surface interactions were observed. Our results do not raise direct reason for concern with respect to crew health, but indicate a potential threat towards material integrity in moist areas.},
}

Archaea/*classification/genetics/isolation & purification
Bacteria/*classification/genetics/isolation & purification
Biodiversity
Biofilms/growth & development
Extremophiles
Fungi/*classification/genetics/isolation & purification
*Health
Host Microbial Interactions
Humans
Metagenomics
Microbiota/genetics/*physiology
Phylogeny
RNA, Ribosomal, 16S/genetics
*Space Flight

@article {pmid31311146,
year = {2019},
author = {Vamanu, E and Pelinescu, D and Gatea, F and Sârbu, I},
title = {Altered in Vitro Metabolomic Response of the Human Microbiota to Sweeteners.},
journal = {Genes},
volume = {10},
number = {7},
pages = {},
doi = {10.3390/genes10070535},
pmid = {31311146},
issn = {2073-4425},
mesh = {Ammonia/metabolism ; Diterpenes, Kaurane/metabolism ; Dysbiosis ; Fatty Acids/metabolism ; Gastrointestinal Microbiome/drug effects ; Humans ; *Metabolome ; *Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Microbiota/*drug effects ; Sweetening Agents/*pharmacology ; },
abstract = {Non-nutritive sweeteners represent an ingredient class that directly affects human health, via the development of inflammatory processes that promote chronic diseases related to microbiota dysbiosis. Several in vitro tests were conducted in the static GIS1 simulator. The aim of the study was to highlight the effect of sweeteners on the microbiota pattern of healthy individuals, associated with any alteration in the metabolomic response, through the production of organic acids and ammonium. The immediate effect of the in vitro treatment and the influence of the specific sweetener type on the occurrence of dysbiosis were evaluated by determining the biomarkers of the microbiota response. The presence of the steviol reduced the ammonium level (minimum of 410 mg/L), while the addition of cyclamate and saccharin caused a decrease in the number of microorganisms, in addition to lowering the total quantity of synthesized short-chain fatty acids (SCFAs). The bifidobacteria appeared to decrease below 102 genomes/mL in all the analyzed samples at the end of the in vitro simulation period. Barring the in vitro treatment of steviol, all the sweeteners tested exerted a negative influence on the fermentative profile, resulting in a decline in the fermentative processes, a rise in the colonic pH, and uniformity of the SCFA ratio.},
}

Ammonia/metabolism
Diterpenes, Kaurane/metabolism
Dysbiosis
Fatty Acids/metabolism
Gastrointestinal Microbiome/drug effects
Humans
*Metabolome
*Metabolomics/methods
Metagenome
Metagenomics/methods
Microbiota/*drug effects
Sweetening Agents/*pharmacology

@article {pmid31197613,
year = {2019},
author = {Debédat, J and Clément, K and Aron-Wisnewsky, J},
title = {Gut Microbiota Dysbiosis in Human Obesity: Impact of Bariatric Surgery.},
journal = {Current obesity reports},
volume = {8},
number = {3},
pages = {229-242},
doi = {10.1007/s13679-019-00351-3},
pmid = {31197613},
issn = {2162-4968},
mesh = {Animals ; Bacteria ; Bariatric Surgery/*methods ; Diabetes Mellitus, Type 2/complications ; Dysbiosis/*complications/*therapy ; Gastrectomy ; Gastrointestinal Microbiome/*physiology ; Humans ; Inflammation ; Obesity/*complications/*surgery ; Obesity, Morbid/complications/surgery ; Postoperative Period ; Treatment Outcome ; Weight Gain ; Weight Loss ; },
abstract = {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.},
}

Animals
Bacteria
Bariatric Surgery/*methods
Diabetes Mellitus, Type 2/complications
Dysbiosis/*complications/*therapy
Gastrectomy
Gastrointestinal Microbiome/*physiology
Humans
Inflammation
Obesity/*complications/*surgery
Obesity, Morbid/complications/surgery
Postoperative Period
Treatment Outcome
Weight Gain
Weight Loss

@article {pmid31153098,
year = {2019},
author = {Farina, R and Severi, M and Carrieri, A and Miotto, E and Sabbioni, S and Trombelli, L and Scapoli, C},
title = {Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions.},
journal = {Archives of oral biology},
volume = {104},
number = {},
pages = {13-23},
doi = {10.1016/j.archoralbio.2019.05.025},
pmid = {31153098},
issn = {1879-1506},
mesh = {*Dental Plaque ; *Diabetes Mellitus, Type 2/complications/microbiology ; Gingiva ; Humans ; *Metagenomics ; *Microbiota ; *Mouth/microbiology ; *Periodontitis/complications/microbiology ; },
abstract = {OBJECTIVE: The aim of this study was to use high-resolution whole metagenomic shotgun sequencing to characterize the subgingival microbiome of patients with/without type 2 Diabetes Mellitus and with/without periodontitis.

DESIGN: Twelve subjects, falling into one of the four study groups based on the presence/absence of poorly controlled type 2 Diabetes Mellitus and moderate-severe periodontitis, were selected. For each eligible subject, subgingival plaque samples were collected at 4 sites, all representative of the periodontal condition of the individual (i.e., non-bleeding sulci in subjects without a history of periodontitis, bleeding pockets in patients with moderate-severe periodontitis). The subgingival microbiome was evaluated using high-resolution whole metagenomic shotgun sequencing.

RESULTS: The results showed that: (i) the presence of type 2 Diabetes Mellitus and/or periodontitis were associated with a tendency of the subgingival microbiome to decrease in richness and diversity; (ii) the presence of type 2 Diabetes Mellitus was not associated with significant differences in the relative abundance of one or more species in patients either with or without periodontitis; (iii) the presence of periodontitis was associated with a significantly higher relative abundance of Anaerolineaceae bacterium oral taxon 439 in type 2 Diabetes Mellitus patients.

CONCLUSIONS: Whole metagenomic shotgun sequencing of the subgingival microbiome was extremely effective in the detection of low-abundant taxon. Our results point out a significantly higher relative abundance of Anaerolineaceae bacterium oral taxon 439 in patients with moderate to severe periodontitis vs patients without history of periodontitis, which was maintained when the comparison was restricted to type 2 diabetics.},
}

*Dental Plaque
*Diabetes Mellitus, Type 2/complications/microbiology
Gingiva
Humans
*Metagenomics
*Microbiota
*Mouth/microbiology
*Periodontitis/complications/microbiology

@article {pmid30599936,
year = {2019},
author = {Danneskiold-Samsøe, NB and Dias de Freitas Queiroz Barros, H and Santos, R and Bicas, JL and Cazarin, CBB and Madsen, L and Kristiansen, K and Pastore, GM and Brix, S and Maróstica Júnior, MR},
title = {Interplay between food and gut microbiota in health and disease.},
journal = {Food research international (Ottawa, Ont.)},
volume = {115},
number = {},
pages = {23-31},
doi = {10.1016/j.foodres.2018.07.043},
pmid = {30599936},
issn = {1873-7145},
mesh = {*Diet ; Dietary Fiber/metabolism ; Dietary Proteins/metabolism ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Lipid Metabolism ; Polyphenols/metabolism ; Prebiotics/analysis ; },
abstract = {Numerous microorganisms colonize the human gastrointestinal tract playing pivotal roles in relation to digestion and absorption of dietary components. They biotransform food components and produce metabolites, which in combination with food components shape and modulate the host immune system and metabolic responses. Reciprocally, the diet modulates the composition and functional capacity of the gut microbiota, which subsequently influence host biochemical processes establishing a system of mutual interaction and inter-dependency. Macronutrients, fibers, as well as polyphenols and prebiotics are strong drivers shaping the composition of the gut microbiota. Especially, short-chain fatty acids produced from ingested fibers and tryptophan metabolites are key in modulating host immune responses. Since reciprocal interactions between diet, host, and microbiota are personal, understanding this complex network of interactions calls for novel use of large datasets and the implementation of machine learning algorithms and artificial intelligence. In this review, we aim to provide a base for future investigations of how interactions between food components and gut microbiota may influence or even determine human health and disease.},
}

*Diet
Dietary Fiber/metabolism
Dietary Proteins/metabolism
Fatty Acids, Volatile/metabolism
*Gastrointestinal Microbiome
Gastrointestinal Tract/*microbiology
Humans
Lipid Metabolism
Polyphenols/metabolism
Prebiotics/analysis

@article {pmid30592383,
year = {2019},
author = {van Dijkhuizen, EHP and Del Chierico, F and Malattia, C and Russo, A and Pires Marafon, D and Ter Haar, NM and Magni-Manzoni, S and Vastert, SJ and Dallapiccola, B and Prakken, B and Martini, A and De Benedetti, F and Putignani, L and , },
title = {Microbiome Analytics of the Gut Microbiota in Patients With Juvenile Idiopathic Arthritis: A Longitudinal Observational Cohort Study.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {71},
number = {6},
pages = {1000-1010},
doi = {10.1002/art.40827},
pmid = {30592383},
issn = {2326-5205},
mesh = {Arthritis, Juvenile/epidemiology/*microbiology ; Case-Control Studies ; Child ; Child, Preschool ; Cohort Studies ; Comorbidity ; Dysbiosis/*epidemiology ; Faecalibacterium prausnitzii ; Female ; Firmicutes ; Gastrointestinal Microbiome/*genetics ; Humans ; Italy/epidemiology ; Logistic Models ; Longitudinal Studies ; Male ; Metagenomics ; Netherlands/epidemiology ; RNA, Ribosomal, 16S ; Severity of Illness Index ; },
abstract = {OBJECTIVE: To assess the composition of gut microbiota in Italian and Dutch patients with juvenile idiopathic arthritis (JIA) at baseline, with inactive disease, and with persistent activity compared to healthy controls.

METHODS: In a multicenter, prospective, observational cohort study, fecal samples were collected at baseline from 78 Italian and 21 Dutch treatment-naive JIA patients with <6 months of disease duration and compared to 107 geographically matched samples from healthy children. Forty-four follow-up samples from patients with inactive disease and 25 follow-up samples from patients with persistent activity were analyzed. Gut microbiota composition was determined by 16S ribosomal RNA-based metagenomics. Alpha- and β-diversity were computed, and log ratios of relative abundance were compared between patients and healthy controls using random forest models and logistic regression.

RESULTS: Baseline samples from Italian patients showed reduced richness compared to healthy controls (P < 0.001). Random forest models distinguished between Italian patient baseline samples and healthy controls and suggested differences between Dutch patient samples and healthy controls (areas under the curve >0.99 and 0.71, respectively). The operational taxonomic units (OTUs) of Erysipelotrichaceae (increased in patients), Allobaculum (decreased in patients), and Faecalibacterium prausnitzii (increased in patients) showed different relative abundance in Italian patient baseline samples compared to controls after controlling for multiple comparisons. Some OTUs differed between Dutch patient samples and healthy controls, but no evidence remained after controlling for multiple comparisons. No differences were found in paired analysis between Italian patient baseline and inactive disease samples.

CONCLUSION: Our findings show evidence for dysbiosis in JIA patients. Only patient/control status, age, and geographic origin appear to be drivers of the microbiota profiles, regardless of disease activity stage, inflammation, and markers of autoimmunity.},
}

Arthritis, Juvenile/epidemiology/*microbiology
Case-Control Studies
Child
Child, Preschool
Cohort Studies
Comorbidity
Dysbiosis/*epidemiology
Faecalibacterium prausnitzii
Female
Firmicutes
Gastrointestinal Microbiome/*genetics
Humans
Italy/epidemiology
Logistic Models
Longitudinal Studies
Male
Metagenomics
Netherlands/epidemiology
RNA, Ribosomal, 16S
Severity of Illness Index

@article {pmid31373310,
year = {2019},
author = {Peric, A and Weiss, J and Vulliemoz, N and Baud, D and Stojanov, M},
title = {Bacterial Colonization of the Female Upper Genital Tract.},
journal = {International journal of molecular sciences},
volume = {20},
number = {14},
pages = {},
doi = {10.3390/ijms20143405},
pmid = {31373310},
issn = {1422-0067},
mesh = {Bacteroidetes/genetics/isolation & purification ; Fallopian Tubes/*microbiology ; Female ; Humans ; Lactobacillus/genetics/*isolation & purification ; Microbiota/physiology ; Ovary/*microbiology ; Placenta/*microbiology ; Pregnancy ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Uterus/*microbiology ; },
abstract = {Bacteria colonize most of the human body, and the female genital tract is not an exception. While the existence of a vaginal microbiota has been well established, the upper genital tract has been considered a sterile environment, with a general assumption that bacterial presence is associated with adverse clinical manifestation. However, recent metagenomic studies identified specific patterns of microbiota colonizing the uterus, fallopian tubes, ovaries, and placenta. These results need confirmation and further investigations since the data are only scarce. Bacterial colonization of these sites appears different from the vaginal one, despite evidence that vaginal bacteria could ascend to the upper genital tract through the cervix. Are these bacteria only commensal or do they play a role in the physiology of the female upper genital tract? Which are the genera that may have a negative and a positive impact on the female reproductive function? The aim of this review is to critically present all available data on upper genital tract microbiota and discuss its role in human reproduction, ranging from the technical aspects of these types of analyses to the description of specific bacterial genera. Although still very limited, research focusing on genital colonization of bacteria other than the vaginal milieu might bring novel insights into physiopathology of human reproduction.},
}

Bacteroidetes/genetics/isolation & purification
Fallopian Tubes/*microbiology
Female
Humans
Lactobacillus/genetics/*isolation & purification
Microbiota/physiology
Ovary/*microbiology
Placenta/*microbiology
Pregnancy
Proteobacteria/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Uterus/*microbiology

@article {pmid31021333,
year = {2019},
author = {Xu, H and Zhao, F and Hou, Q and Huang, W and Liu, Y and Zhang, H and Sun, Z},
title = {Metagenomic analysis revealed beneficial effects of probiotics in improving the composition and function of the gut microbiota in dogs with diarrhoea.},
journal = {Food & function},
volume = {10},
number = {5},
pages = {2618-2629},
doi = {10.1039/c9fo00087a},
pmid = {31021333},
issn = {2042-650X},
mesh = {Animals ; Bacteria/classification/drug effects/*genetics/isolation & purification ; Diarrhea/drug therapy/microbiology/*veterinary ; Dog Diseases/*drug therapy/microbiology ; Dogs ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Metagenomics ; Phylogeny ; Probiotics/*administration & dosage ; },
abstract = {The aim of the present study was to evaluate the effects of probiotics on the composition and function of the gut microbiota in dogs with diarrhoea. Forty dogs with diarrhoea were randomly allocated to the treatment group or control group. Probiotics, containing Lactobacillus casei Zhang, Lactobacillus plantarum P-8, and Bifidobacterium animalis subsp. lactis V9, were only fed to 20 treated dogs for 60 days. The faecal samples of all dogs at day 0 and day 60 were analyzed using a metagenomic approach. The results showed a significantly higher microbial diversity and an obvious change in the structure of the gut microbiota in the treatment group. There was also an increase in the abundance of some beneficial bacteria in differently aged dogs, such as Lactobacillus johnsonii (P < 0.05), Lactobacillus reuteri (P < 0.01), Lactobacillus acidophilus (P < 0.05) and Butyricicoccus pullicaecorum (P < 0.05), and a reduction in the abundance of many opportunistic pathogenic bacteria such as Clostridium perfringens (P < 0.05) and Stenotrophomonas maltophilia (P < 0.05) with the supplementation of probiotics. Intriguingly, the correlated networks among some pathogenic bacteria decreased following the administration of probiotics. Additionally, metagenomic analysis revealed the upregulation of pathways involved in the metabolism of amino acids and biosynthesis of secondary metabolites, accompanied by the downregulation of pathways associated with virulence of pathogenic bacteria and cell signaling, suggesting that probiotics could improve the health of dogs with diarrhoea through regulation of the gut microbiota. Our research provides new information relevant to the treatment of diarrhoea in animals and humans.},
}

Animals
Bacteria/classification/drug effects/*genetics/isolation & purification
Diarrhea/drug therapy/microbiology/*veterinary
Dog Diseases/*drug therapy/microbiology
Dogs
Feces/microbiology
Gastrointestinal Microbiome/*drug effects
Metagenomics
Phylogeny
Probiotics/*administration & dosage

@article {pmid30810996,
year = {2019},
author = {Pérez-Fernández, CA and Iriarte, M and Rivera-Pérez, J and Tremblay, RL and Toranzos, GA},
title = {Microbiota dispersion in the Uyuni salt flat (Bolivia) as determined by community structure analyses.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {22},
number = {3},
pages = {325-336},
doi = {10.1007/s10123-018-00052-2},
pmid = {30810996},
issn = {1618-1905},
support = {5R25GM061151-12, -13//Research Initiative for Scientific Enhancement Program/ ; },
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biota ; Bolivia ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {Soil microbial communities are an important component of biological diversity and terrestrial ecosystems which is responsible for processes such as decomposition, mineralization of nutrients, and accumulation of organic matter. One of the factors that provide information on the mechanisms regulating biodiversity is spatial scaling. We characterized the microbial communities using 16S rRNA gene sequences from DNA isolated from halite at various locations and correlated these to geographic distance in the Uyuni salt flat (Bolivia). Sequences from each site were analyzed to determine any spatial patterns of diversity, as well as to describe the microbial communities. Results suggest that different taxa are able to disperse over Uyuni's surface crust regardless of distance. As expected, ubiquitous taxa included members of Halobacteriaceae such as Haloarcula, Halorubrum, Halorhabdus, Halolamina, and halophilic bacteria Salinibacter, Halorhodospira, and unclassified members of the Gammaproteobacteria. Archaeal communities were homogeneous across the salt flat. In contrast, bacterial communities present strong local variations which could be attributed to external factors. Likely sources for these variations are the Rio Grande river influent in the south shore and the Tunupa volcano influencing the northern area.},
}

Archaea/*classification/genetics
Bacteria/*classification/genetics
*Biota
Bolivia
Cluster Analysis
DNA, Archaeal/chemistry/genetics
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
Metagenomics
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
*Soil Microbiology

@article {pmid30738924,
year = {2019},
author = {Wang, Y and Liu, F and Urban, JF and Paerewijck, O and Geldhof, P and Li, RW},
title = {Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome.},
journal = {International journal for parasitology},
volume = {49},
number = {3-4},
pages = {247-256},
doi = {10.1016/j.ijpara.2018.10.007},
pmid = {30738924},
issn = {1879-0135},
mesh = {Animals ; Ascariasis/complications/epidemiology/*veterinary ; Ascaris suum/*isolation & purification ; Cluster Analysis ; Colon/microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Dysbiosis/epidemiology/*veterinary ; Fatty Acids, Volatile/analysis ; Feces/chemistry/microbiology ; *Gastrointestinal Microbiome ; Metabolomics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Swine ; Swine Diseases/*epidemiology ; },
abstract = {The effect of infection of pigs with Ascaris suum on the microbial composition in the proximal colon and fecal matter was investigated using 16S rRNA gene sequencing. The infection significantly decreased various microbial diversity indices including Chao1 richness, but the effect on Chao1 in the colon luminal contents was worm burden-independent. The abundance of 49 genera present in colon contents, such as Prevotella and Faecalibacterium, and 179 operational taxonomic units was significantly changed as a result of infection. Notably, infection was also associated with a significant shift in the metabolic potential of the proximal colon microbiome, where the relative abundance of at least 30 metabolic pathways including carbohydrate metabolism and amino acid metabolism was reduced, while the abundance of 28 pathways was increased by infection. Furthermore, the microbial co-occurrence network in infected pigs was highly modular. Two of 52 modules or subnetworks were negatively correlated with fecal butyrate concentrations (r < -0.7; P < 0.05) while one module with 18 members was negatively correlated with fecal acetate, propionate and total short-chain fatty acids. A partial Mantel test identified a strong positive correlation between node connectivity of the operational taxonomic units assigned to β-Proteobacteria (especially the family Alcaligenaceae) and fecal acetate and propionate levels (r = 0.82 and 0.74, respectively), while that of the family Porphyromonadaceae was positively correlated with fecal egg counts. Overall, Ascaris infection was associated with a profound change in the gut microbiome, especially in the proximity of the initial site of larval infection, and should facilitate our understanding of the pathophysiological consequence of gastrointestinal nematode infections.},
}

Animals
Ascariasis/complications/epidemiology/*veterinary
Ascaris suum/*isolation & purification
Cluster Analysis
Colon/microbiology
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
Dysbiosis/epidemiology/*veterinary
Fatty Acids, Volatile/analysis
Feces/chemistry/microbiology
*Gastrointestinal Microbiome
Metabolomics
Metagenomics
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Swine
Swine Diseases/*epidemiology

@article {pmid31892895,
year = {2019},
author = {Vinas, N and Thrash, A and Ii, MA and Jones, R and Douglas, T and Perkins, E},
title = {Keanu: A Novel Visualization Tool to Explore Biodiversity in Metagenomes.},
journal = {Journal of biomolecular techniques : JBT},
volume = {30},
number = {Suppl},
pages = {S24},
pmid = {31892895},
issn = {1943-4731},
abstract = {One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. Here, we describe development and application of a command-line tool for exploring sample content in metagenomics data. Keanu, a tool for exploring sequence content, allows a user to understand what organisms are present in a sample and their abundance by analyzing alignments against a BLAST database and displaying them in an interactive web page. The content of a sample can be presented as a collapsible tree, with node sizes indicating abundance, or a bilevel partition graph, with arc size indicating abundance.Here, we show how we used Keanu to explore shotgun metagenomics data from a sample collected from a bluff that contained paleosols in an alpine site in interior Alaska. The site contained a krotovina, which is an ancient nest of unknown origin. Keanu allowed us to explore the potential origin of the krotovina by visualizing the number of hits related to different taxonomic categories. In summary, Keanu provides a facile means by which researchers can explore and visualize species present in sequence data generated from complex communities and environments. Keanu is written in Python and is freely available at https://github.com/IGBB/keanu.},
}

@article {pmid31734392,
year = {2020},
author = {Li, W and Zhuang, JL and Zhou, YY and Meng, FG and Kang, D and Zheng, P and Shapleigh, JP and Liu, YD},
title = {Metagenomics reveals microbial community differences lead to differential nitrate production in anammox reactors with differing nitrogen loading rates.},
journal = {Water research},
volume = {169},
number = {},
pages = {115279},
doi = {10.1016/j.watres.2019.115279},
pmid = {31734392},
issn = {1879-2448},
mesh = {Bioreactors ; Denitrification ; Metagenomics ; *Microbiota ; *Nitrogen ; Oxidation-Reduction ; },
abstract = {Nitrate production during anammox can decrease total nitrogen removal efficiency, which will negatively impact its usefulness for the removal of nitrogen from waste streams. However, neither the performance characteristics nor physiological shifts associated with nitrate accumulation in anammox reactors under different nitrogen loading rates (NLRs) is well understood. Consequently, these parameters were studied in a lower NLR anammox reactor, termed R1, producing higher than expected levels of nitrate and compared with a higher NLR reactor, termed R2, showing no excess nitrate production. While both reactors showed high NH4+-N removal efficiencies (>90%), the total nitrogen removal efficiency (<60%) was much lower in R1 due to higher nitrate production. Metagenomic analysis found that the number of reads derived from anammox bacteria were significantly higher in R2. Another notable trend in reads occurrence was the relatively higher levels of reads from genes predicted to be nitrite oxidoreductases (nxr) in R1. Binning yielded 27 high quality draft genomes from the two reactors. Analysis of bin occurrence found that R1 showing both a decrease in anammox bacteria and an unexpected increase in nxr. In-situ assays confirmed that R1 had higher rates of nitrite oxidation to nitrate and suggested that it was not solely due to obligate NOB, but other nxr-containing bacteria are important contributors as well. Our results demonstrate that nitrate accumulation can be a serious operational concern for the application of anammox technology to low-strength wastewater treatment and provide insight into the community changes leading to this outcome.},
}

Bioreactors
Denitrification
Metagenomics
*Microbiota
*Nitrogen
Oxidation-Reduction

@article {pmid31226275,
year = {2019},
author = {Assié, A and Samuel, BS},
title = {The Devil Is in the Microbial Genetic Details.},
journal = {Molecular cell},
volume = {74},
number = {6},
pages = {1108-1109},
doi = {10.1016/j.molcel.2019.06.003},
pmid = {31226275},
issn = {1097-4164},
mesh = {*Gastrointestinal Microbiome ; Genetics, Microbial ; Humans ; },
abstract = {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.},
}

*Gastrointestinal Microbiome
Genetics, Microbial
Humans

@article {pmid31884983,
year = {2019},
author = {Traoré, SI and Bilen, M and Cadoret, F and Khelaifia, S and Million, M and Raoult, D and Lagier, JC},
title = {Study of Human Gastrointestinal Microbiota by Culturomics in Africa.},
journal = {Medecine et sante tropicales},
volume = {29},
number = {4},
pages = {366-370},
doi = {10.1684/mst.2019.0943},
pmid = {31884983},
issn = {2261-2211},
abstract = {The interest in studying gut microbiota has been rekindled with the advent of molecular techniques, in particular, metagenomics. Culturomics (high throughput microbial culture with identification of the colonies by Maldi-TOF) has demonstrated its complementarity with metagenomics for comprehensive study of the microbiota. The main metagenomic studies have revealed an increase in biodiversity, with in particular an increase of Spirochaetes and Prevotella in subjects of African origin compared with Western subjects. Studies on malnutrition have shown a reduction of all bacteria and in particular of anaerobic bacteria and methanogenic archaea. Of the 1,162 bacteria isolated by culturomics studies, 476 were isolated only from non-African samples, 445 were isolated in African and non-African groups, and 241 bacteria were isolated from samples of African origin including 68 new species. Further studies of African microbiota by culturomics and metagenomics will make it possible to assess whether some bacteria have particular specificities and if these might play a role in certain pathologies such as malnutrition.},
}

@article {pmid31884971,
year = {2019},
author = {Coutinho, FH and Edwards, RA and Rodríguez-Valera, F},
title = {Charting the diversity of uncultured viruses of Archaea and Bacteria.},
journal = {BMC biology},
volume = {17},
number = {1},
pages = {109},
doi = {10.1186/s12915-019-0723-8},
pmid = {31884971},
issn = {1741-7007},
support = {APOSTD/2018/186//Conselleria d'Educació, Investigació, Cultura i Esport/ ; GL2016-76273-P//Ministerio de Economía y Competitividad/ ; CGL2015-71523-REDC//Ministerio de Economía y Competitividad/ ; },
abstract = {BACKGROUND: Viruses of Archaea and Bacteria are among the most abundant and diverse biological entities on Earth. Unraveling their biodiversity has been challenging due to methodological limitations. Recent advances in culture-independent techniques, such as metagenomics, shed light on the unknown viral diversity, revealing thousands of new viral nucleotide sequences at an unprecedented scale. However, these novel sequences have not been properly classified and the evolutionary associations between them were not resolved.

RESULTS: Here, we performed phylogenomic analysis of nearly 200,000 viral nucleotide sequences to establish GL-UVAB: Genomic Lineages of Uncultured Viruses of Archaea and Bacteria. The pan-genome content of the identified lineages shed light on some of their infection strategies, potential to modulate host physiology, and mechanisms to escape host resistance systems. Furthermore, using GL-UVAB as a reference database for annotating metagenomes revealed elusive habitat distribution patterns of viral lineages and environmental drivers of community composition.

CONCLUSIONS: These findings provide insights about the genomic diversity and ecology of viruses of prokaryotes. The source code used in these analyses is freely available at https://sourceforge.net/projects/gluvab/.},
}

@article {pmid31181638,
year = {2019},
author = {Astó, E and Méndez, I and Rodríguez-Prado, M and Cuñé, J and Espadaler, J and Farran-Codina, A},
title = {Effect of the Degree of Polymerization of Fructans on Ex Vivo Fermented Human Gut Microbiome.},
journal = {Nutrients},
volume = {11},
number = {6},
pages = {},
doi = {10.3390/nu11061293},
pmid = {31181638},
issn = {2072-6643},
mesh = {Adult ; Bacteria/*drug effects/growth & development ; Bacterial Typing Techniques/methods ; Colon/microbiology ; Female ; Fermentation ; Fructans/chemistry/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Inulin/chemistry/pharmacology ; Male ; Oligosaccharides/chemistry/*pharmacology ; *Polymerization ; *Prebiotics ; },
abstract = {Prebiotic supplements are used to promote gastrointestinal health by stimulating beneficial bacteria. The aim of this study was to compare the potential prebiotic effects of fructans with increasing degrees of polymerization, namely fructooligosaccharides (FOS) and inulins with a low and high polymerization degree (LPDI and HPDI, respectively), using an ex vivo fermentation system to simulate the colonic environment. The system was inoculated with pooled feces from three healthy donors with the same baseline enterotype. Changes in microbiota composition were measured by 16S metagenomic sequencing after 2, 7, and 14 days of fermentation, and acid production was measured throughout the experiment. Alpha-diversity decreased upon inoculation of the ex vivo fermentation under all treatments. Composition changed significantly across both treatments and time (ANOSIM p < 0.005 for both factors). HPDI and LPDI seemed to be similar to each other regarding composition and acidification activity, but different from the control and FOS. FOS differed from the control in terms of composition but not acidification. HDPI restored alpha-diversity on day 14 as compared to the control (Bonferroni p < 0.05). In conclusion, the prebiotic activity of fructans appears to depend on the degree of polymerization, with LPDI and especially HPDI having a greater effect than FOS.},
}

Adult
Bacteria/*drug effects/growth & development
Bacterial Typing Techniques/methods
Colon/microbiology
Female
Fermentation
Fructans/chemistry/*pharmacology
Gastrointestinal Microbiome/*drug effects
Humans
Inulin/chemistry/pharmacology
Male
Oligosaccharides/chemistry/*pharmacology
*Polymerization
*Prebiotics

@article {pmid30832245,
year = {2019},
author = {Cortes-Rodriguez, N and Campana, MG and Berry, L and Faegre, S and Derrickson, SR and Ha, RR and Dikow, RB and Rutz, C and Fleischer, RC},
title = {Population Genomics and Structure of the Critically Endangered Mariana Crow (Corvus kubaryi).},
journal = {Genes},
volume = {10},
number = {3},
pages = {},
doi = {10.3390/genes10030187},
pmid = {30832245},
issn = {2073-4425},
support = {BB/G023913/2//Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship/International ; },
mesh = {Animals ; Conservation of Natural Resources ; Crows/*classification/genetics ; Endangered Species ; Evolution, Molecular ; Female ; Guam ; High-Throughput Nucleotide Sequencing ; Male ; Metagenomics/*methods ; Phylogeography ; Polymorphism, Single Nucleotide ; Whole Genome Sequencing/*methods ; },
abstract = {The Mariana Crow, or Åga (Corvus kubaryi), is a critically endangered species (IUCN -International Union for Conservation of Nature), endemic to the islands of Guam and Rota in the Mariana Archipelago. It is locally extinct on Guam, and numbers have declined dramatically on Rota to a historical low of less than 55 breeding pairs throughout the island in 2013. Because of its extirpation on Guam and population decline on Rota, it is of critical importance to assess the genetic variation among individuals to assist ongoing recovery efforts. We conducted a population genomics analysis comparing the Guam and Rota populations and studied the genetic structure of the Rota population. We used blood samples from five birds from Guam and 78 birds from Rota. We identified 145,552 candidate single nucleotide variants (SNVs) from a genome sequence of an individual from Rota and selected a subset of these to develop an oligonucleotide in-solution capture assay. The Guam and Rota populations were genetically differentiated from each other. Crow populations sampled broadly across their range on Rota showed significant genetic structuring ⁻ a surprising result given the small size of this island and the good flight capabilities of the species. Knowledge of its genetic structure will help improve management strategies to help with its recovery.},
}

Animals
Conservation of Natural Resources
Crows/*classification/genetics
Endangered Species
Evolution, Molecular
Female
Guam
High-Throughput Nucleotide Sequencing
Male
Metagenomics/*methods
Phylogeography
Polymorphism, Single Nucleotide
Whole Genome Sequencing/*methods

@article {pmid29572891,
year = {2018},
author = {Caussy, C and Hsu, C and Lo, MT and Liu, A and Bettencourt, R and Ajmera, VH and Bassirian, S and Hooker, J and Sy, E and Richards, L and Schork, N and Schnabl, B and Brenner, DA and Sirlin, CB and Chen, CH and Loomba, R and , },
title = {Link between gut-microbiome derived metabolite and shared gene-effects with hepatic steatosis and fibrosis in NAFLD.},
journal = {Hepatology (Baltimore, Md.)},
volume = {68},
number = {3},
pages = {918-932},
pmid = {29572891},
issn = {1527-3350},
support = {//American Gastroenterological Association (AGA) Foundation- Sucampo - ASP Designated Research Award in Geriatric Gastroenterology/International ; //T. Franklin Williams Scholarship Award/International ; //Atlantic Philanthropies, Inc/International ; //John A. Hartford Foundation/International ; //OM/International ; //Association of Specialty Professors/International ; K23-DK090303//American Gastroenterological Association/International ; R01-DK106419//American Gastroenterological Association/International ; //Société Francophone du Diabète (SFD)/International ; //Philippe Foundation and Monahan Foundation/International ; //Fulbright program/International ; K23 DK090303/DK/NIDDK NIH HHS/United States ; KL2 RR031978/RR/NCRR NIH HHS/United States ; P42 ES010337/ES/NIEHS NIH HHS/United States ; R01 DK106419/DK/NIDDK NIH HHS/United States ; },
mesh = {Adult ; Aged ; Cross-Sectional Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Liver Cirrhosis/*blood/microbiology ; Male ; Metformin ; Middle Aged ; Non-alcoholic Fatty Liver Disease/*blood/microbiology ; Phenylpropionates/*blood ; Proof of Concept Study ; },
abstract = {Previous studies have shown that gut-microbiome is associated with nonalcoholic fatty liver disease (NAFLD). We aimed to examine if serum metabolites, especially those derived from the gut-microbiome, have a shared gene-effect with hepatic steatosis and fibrosis. This is a cross-sectional analysis of a prospective discovery cohort including 156 well-characterized twins and families with untargeted metabolome profiling assessment. Hepatic steatosis was assessed using magnetic-resonance-imaging proton-density-fat-fraction (MRI-PDFF) and fibrosis using MR-elastography (MRE). A twin additive genetics and unique environment effects (AE) model was used to estimate the shared gene-effect between metabolites and hepatic steatosis and fibrosis. The findings were validated in an independent prospective validation cohort of 156 participants with biopsy-proven NAFLD including shotgun metagenomics sequencing assessment in a subgroup of the cohort. In the discovery cohort, 56 metabolites including 6 microbial metabolites had a significant shared gene-effect with both hepatic steatosis and fibrosis after adjustment for age, sex and ethnicity. In the validation cohort, 6 metabolites were associated with advanced fibrosis. Among them, only one microbial metabolite, 3-(4-hydroxyphenyl)lactate, remained consistent and statistically significantly associated with liver fibrosis in the discovery and validation cohort (fold-change of higher-MRE versus lower-MRE: 1.78, P < 0.001 and of advanced versus no advanced fibrosis: 1.26, P = 0.037, respectively). The share genetic determination of 3-(4-hydroxyphenyl)lactate with hepatic steatosis was RG :0.57,95%CI:0.27-0.80, P < 0.001 and with fibrosis was RG :0.54,95%CI:0.036-1, P = 0.036. Pathway reconstruction linked 3-(4-hydroxyphenyl)lactate to several human gut-microbiome species. In the validation cohort, 3-(4-hydroxyphenyl)lactate was significantly correlated with the abundance of several gut-microbiome species, belonging only to Firmicutes, Bacteroidetes and Proteobacteria phyla, previously reported as associated with advanced fibrosis. Conclusion: This proof of concept study provides evidence of a link between the gut-microbiome and 3-(4-hydroxyphenyl)lactate that shares gene-effect with hepatic steatosis and fibrosis. (Hepatology 2018).},
}

Adult
Aged
Cross-Sectional Studies
Female
*Gastrointestinal Microbiome
Humans
Liver Cirrhosis/*blood/microbiology
Male
Metformin
Middle Aged
Non-alcoholic Fatty Liver Disease/*blood/microbiology
Phenylpropionates/*blood
Proof of Concept Study

@article {pmid31159288,
year = {2019},
author = {Couto-Rodríguez, RL and Montalvo-Rodríguez, R},
title = {Temporal Analysis of the Microbial Community from the Crystallizer Ponds in Cabo Rojo, Puerto Rico, Using Metagenomics.},
journal = {Genes},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/genes10060422},
pmid = {31159288},
issn = {2073-4425},
support = {52007566/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Bacteroidetes/genetics ; Euryarchaeota/genetics ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; *Phylogeny ; Ponds/microbiology ; Proteobacteria/genetics ; Puerto Rico ; Tropical Climate ; Water Microbiology ; },
abstract = {The Cabo Rojo solar salterns are a hypersaline environment located in a tropical climate, where conditions remain stable throughout the year. These conditions can favor the establishment of steady microbial communities. Little is known about the microbial composition that thrives in hypersaline environments in the tropics. The main goal of this study was to assess the microbial diversity present in the crystallizer ponds of Cabo Rojo, in terms of structure and metabolic processes across time using metagenomic techniques. Three samplings (December 2014, March and July 2016) were carried out, where water samples (50 L each) were filtered through a Millipore pressurized filtering system. DNA was subsequently extracted using physical-chemical methods and sequenced using paired end Illumina technologies. The sequencing effort produced three paired end libraries with a total of 111,816,040 reads, that were subsequently assembled into three metagenomes. Out of the phyla detected, the microbial diversity was dominated in all three samples by Euryarchaeota, followed by Bacteroidetes and Proteobacteria. However, sample MFF1 (for Muestreo Final Fraternidad) exhibited a higher diversity, with 12 prokaryotic phyla detected at 34% NaCl (w/v), when compared to samples MFF2 and MFF3, which only exhibited three phyla. Precipitation events might be one of the contributing factors to the change in the microbial community composition through time. Diversity at genus level revealed a more stable community structure, with an overwhelming dominance of the square archaeon Haloquadratum in the three metagenomes. Furthermore, functional annotation was carried out in order to detect genes related to metabolic processes, such as carbon, nitrogen, and sulfur cycles. The presence of gene sequences related to nitrogen fixation, ammonia oxidation, sulfate reduction, sulfur oxidation, and phosphate solubilization were detected. Through binning methods, four putative novel genomes were obtained, including a possible novel genus belonging to the Bacteroidetes and possible new species for the genera Natronomonas, Halomicrobium, and Haloquadratum. Using a metagenomic approach, a 3-year study has been performed in a Caribbean hypersaline environment. When compared to other salterns around the world, the Cabo Rojo salterns harbor a similar community composition, which is stable through time. Moreover, an analysis of gene composition highlights the importance of the microbial community in the biogeochemical cycles at hypersaline environments.},
}

Bacteroidetes/genetics
Euryarchaeota/genetics
Metagenome/*genetics
*Metagenomics
Microbiota/*genetics
*Phylogeny
Ponds/microbiology
Proteobacteria/genetics
Puerto Rico
Tropical Climate
Water Microbiology

@article {pmid31035394,
year = {2019},
author = {Jaswal, R and Pathak, A and Edwards, B and Lewis, R and Seaman, JC and Stothard, P and Krivushin, K and Blom, J and Rupp, O and Chauhan, A},
title = {Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA.},
journal = {Genes},
volume = {10},
number = {5},
pages = {},
doi = {10.3390/genes10050325},
pmid = {31035394},
issn = {2073-4425},
mesh = {Ascomycota/genetics/radiation effects ; Biodegradation, Environmental ; Burkholderia/genetics/radiation effects ; Ecosystem ; Grassland ; Humans ; Metagenomics ; Microbiota/*genetics/radiation effects ; Penicillium/genetics/radiation effects ; Rivers ; *Soil Microbiology ; United States ; Uranium/*toxicity ; },
abstract = {Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.},
}

Ascomycota/genetics/radiation effects
Biodegradation, Environmental
Burkholderia/genetics/radiation effects
Ecosystem
Grassland
Humans
Metagenomics
Microbiota/*genetics/radiation effects
Penicillium/genetics/radiation effects
Rivers
*Soil Microbiology
United States
Uranium/*toxicity

@article {pmid31207997,
year = {2019},
author = {Garrido-Sanz, D and Redondo-Nieto, M and Guirado, M and Pindado Jiménez, O and Millán, R and Martin, M and Rivilla, R},
title = {Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil.},
journal = {Genes},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/genes10060456},
pmid = {31207997},
issn = {2073-4425},
mesh = {*Biodegradation, Environmental ; Biodiversity ; Chryseobacterium/classification/genetics ; Metagenome/*genetics ; Microbiota/*genetics ; Petroleum/*metabolism ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/metabolism/toxicity ; Pseudomonas/classification/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Soil Pollutants/metabolism/toxicity ; },
abstract = {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.},
}

*Biodegradation, Environmental
Biodiversity
Chryseobacterium/classification/genetics
Metagenome/*genetics
Microbiota/*genetics
Petroleum/*metabolism
Phylogeny
Polycyclic Aromatic Hydrocarbons/metabolism/toxicity
Pseudomonas/classification/genetics/metabolism
RNA, Ribosomal, 16S/genetics
Soil Microbiology
Soil Pollutants/metabolism/toxicity

@article {pmid30624643,
year = {2019},
author = {Baldrian, P},
title = {The known and the unknown in soil microbial ecology.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {2},
pages = {},
doi = {10.1093/femsec/fiz005},
pmid = {30624643},
issn = {1574-6941},
mesh = {Bacteria/*classification/enzymology/genetics ; Ecology ; Ecosystem ; Fungi/*classification/enzymology/genetics ; Metabolomics ; Metagenomics ; Microbiota/*genetics ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {The methodical developments in the fields of molecular biology and analytical chemistry significantly increased the level of detail that we achieve when exploring soils and their microbial inhabitants. High-resolution description of microbial communities, detection of taxa with minor abundances, screening of gene expression or the detailed characterization of metabolomes are nowadays technically feasible. Despite all of this, our understanding of soil is limited in many ways. The imperfect tools to describe microbial communities and limited possibilities to assign traits to community members make it difficult to link microbes to functions. Also the analysis of processes exemplified by enzyme activity measurements is still imperfect. In the future, it is important to look at soil at a finer detail to obtain a better picture on the properties of individual microbes, their in situ interactions, metabolic rates and activity at a scale relevant to individual microbes. Scaling up is needed as well to get answers at ecosystem or biome levels and to enable global modelling. The recent development of novel tools including metabolomics, identification of genomes in metagenomics sequencing datasets or collection of trait data have the potential to bring soil ecology further. It will, however, always remain a highly demanding scientific discipline.},
}

Bacteria/*classification/enzymology/genetics
Ecology
Ecosystem
Fungi/*classification/enzymology/genetics
Metabolomics
Metagenomics
Microbiota/*genetics
Soil/*chemistry
*Soil Microbiology

@article {pmid31873124,
year = {2019},
author = {Ottoni, C and Guellil, M and Ozga, AT and Stone, AC and Kersten, O and Bramanti, B and Porcier, S and Van Neer, W},
title = {Metagenomic analysis of dental calculus in ancient Egyptian baboons.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {19637},
doi = {10.1038/s41598-019-56074-x},
pmid = {31873124},
issn = {2045-2322},
abstract = {Dental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals' oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9th-6th centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons' oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.},
}

@article {pmid31316056,
year = {2019},
author = {Mallick, H and Franzosa, EA and Mclver, LJ and Banerjee, S and Sirota-Madi, A and Kostic, AD and Clish, CB and Vlamakis, H and Xavier, RJ and Huttenhower, C},
title = {Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {3136},
doi = {10.1038/s41467-019-10927-1},
pmid = {31316056},
issn = {2041-1723},
support = {P30 DK036836/DK/NIDDK NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; },
mesh = {Algorithms ; Colitis, Ulcerative/microbiology ; Crohn Disease/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metabolomics ; Metagenomics ; Microbiota/*genetics ; *Models, Genetic ; },
abstract = {Microbial community metabolomics, particularly in the human gut, are beginning to provide a new route to identify functions and ecology disrupted in disease. However, these data can be costly and difficult to obtain at scale, while amplicon or shotgun metagenomic sequencing data are readily available for populations of many thousands. Here, we describe a computational approach to predict potentially unobserved metabolites in new microbial communities, given a model trained on paired metabolomes and metagenomes from the environment of interest. Focusing on two independent human gut microbiome datasets, we demonstrate that our framework successfully recovers community metabolic trends for more than 50% of associated metabolites. Similar accuracy is maintained using amplicon profiles of coral-associated, murine gut, and human vaginal microbiomes. We also provide an expected performance score to guide application of the model in new samples. Our results thus demonstrate that this 'predictive metabolomic' approach can aid in experimental design and provide useful insights into the thousands of community profiles for which only metagenomes are currently available.},
}

Algorithms
Colitis, Ulcerative/microbiology
Crohn Disease/microbiology
Gastrointestinal Microbiome/*genetics
Humans
*Metabolomics
Metagenomics
Microbiota/*genetics
*Models, Genetic

@article {pmid31211676,
year = {2019},
author = {Langelier, C and Graves, M and Kalantar, K and Caldera, S and Durrant, R and Fisher, M and Backman, R and Tanner, W and DeRisi, JL and Leung, DT},
title = {Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers.},
journal = {Emerging infectious diseases},
volume = {25},
number = {7},
pages = {1380-1383},
doi = {10.3201/eid2507.181492},
pmid = {31211676},
issn = {1080-6059},
support = {K23 HL138461/HL/NHLBI NIH HHS/United States ; },
mesh = {Biodiversity ; Communicable Diseases/*epidemiology/*microbiology ; Computational Biology/methods ; Databases, Genetic ; *Drug Resistance, Microbial ; Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Metagenomics/methods ; *Microbiota/drug effects/genetics ; *Travel ; *Travel-Related Illness ; },
abstract = {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.},
}

Biodiversity
Communicable Diseases/*epidemiology/*microbiology
Computational Biology/methods
Databases, Genetic
*Drug Resistance, Microbial
Gene Transfer, Horizontal
High-Throughput Nucleotide Sequencing
Humans
Metagenome
*Metagenomics/methods
*Microbiota/drug effects/genetics
*Travel
*Travel-Related Illness

@article {pmid31194939,
year = {2019},
author = {Johnson, AJ and Vangay, P and Al-Ghalith, GA and Hillmann, BM and Ward, TL and Shields-Cutler, RR and Kim, AD and Shmagel, AK and Syed, AN and , and Walter, J and Menon, R and Koecher, K and Knights, D},
title = {Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans.},
journal = {Cell host & microbe},
volume = {25},
number = {6},
pages = {789-802.e5},
doi = {10.1016/j.chom.2019.05.005},
pmid = {31194939},
issn = {1934-6069},
mesh = {Adult ; *Diet ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Young Adult ; },
abstract = {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.},
}

Adult
*Diet
Feces/microbiology
Female
*Gastrointestinal Microbiome
Humans
Longitudinal Studies
Male
Metagenomics
*Microbiota
Middle Aged
Young Adult

@article {pmid31089679,
year = {2019},
author = {Nicholls, SM and Quick, JC and Tang, S and Loman, NJ},
title = {Ultra-deep, long-read nanopore sequencing of mock microbial community standards.},
journal = {GigaScience},
volume = {8},
number = {5},
pages = {},
doi = {10.1093/gigascience/giz043},
pmid = {31089679},
issn = {2047-217X},
support = {//Medical Research Council/United Kingdom ; //Department of Health/United Kingdom ; },
mesh = {*Metagenome ; Metagenomics/*methods/standards ; Microbiota/*genetics ; Nanopore Sequencing/*methods/standards ; Reference Standards ; },
abstract = {BACKGROUND: Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, and consequently have great potential for the study of microbial communities. However, the best approaches for analysis of long-read metagenomic data are unknown. Additionally, rigorous evaluation of bioinformatics tools is hindered by a lack of long-read data from validated samples with known composition.

FINDINGS: We sequenced 2 commercially available mock communities containing 10 microbial species (ZymoBIOMICS Microbial Community Standards) with Oxford Nanopore GridION and PromethION. Both communities and the 10 individual species isolates were also sequenced with Illumina technology. We generated 14 and 16 gigabase pairs from 2 GridION flowcells and 150 and 153 gigabase pairs from 2 PromethION flowcells for the evenly distributed and log-distributed communities, respectively. Read length N50 ranged between 5.3 and 5.4 kilobase pairs over the 4 sequencing runs. Basecalls and corresponding signal data are made available (4.2 TB in total). Alignment to Illumina-sequenced isolates demonstrated the expected microbial species at anticipated abundances, with the limit of detection for the lowest abundance species below 50 cells (GridION). De novo assembly of metagenomes recovered long contiguous sequences without the need for pre-processing techniques such as binning.

CONCLUSIONS: We present ultra-deep, long-read nanopore datasets from a well-defined mock community. These datasets will be useful for those developing bioinformatics methods for long-read metagenomics and for the validation and comparison of current laboratory and software pipelines.},
}

*Metagenome
Metagenomics/*methods/standards
Microbiota/*genetics
Nanopore Sequencing/*methods/standards
Reference Standards

@article {pmid30872807,
year = {2019},
author = {Thomas, F and Corre, E and Cébron, A},
title = {Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil.},
journal = {The ISME journal},
volume = {13},
number = {7},
pages = {1814-1830},
doi = {10.1038/s41396-019-0394-z},
pmid = {30872807},
issn = {1751-7370},
mesh = {Bacteria/genetics/*isolation & purification/metabolism ; Biodegradation, Environmental ; Carbon Isotopes/analysis ; Lolium/*microbiology ; *Metagenomics ; *Microbial Consortia ; Phenanthrenes/*analysis ; Plant Roots/metabolism ; Polycyclic Aromatic Hydrocarbons/*analysis ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*analysis ; Sphingomonadaceae/genetics/isolation & purification/metabolism ; },
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13C-SIP incubations compared to 12C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil. Active PHE-degraders were taxonomically diverse (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively. Plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level. Indeed, metagenomes of 13C-enriched DNA fractions contained more genes involved in aromatic compound metabolism in bare soil, whereas carbohydrate catabolism genes were more abundant in planted soil. Functional gene annotation allowed reconstruction of complete pathways with several routes for PHE catabolism. Sphingomonadales were the major taxa performing the first steps of PHE degradation in both conditions, suggesting their critical role to initiate in situ PAH remediation. Active PHE-degraders act in a consortium, whereby complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps. Our study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils.},
}

Bacteria/genetics/*isolation & purification/metabolism
Biodegradation, Environmental
Carbon Isotopes/analysis
Lolium/*microbiology
*Metagenomics
*Microbial Consortia
Phenanthrenes/*analysis
Plant Roots/metabolism
Polycyclic Aromatic Hydrocarbons/*analysis
Soil/chemistry
Soil Microbiology
Soil Pollutants/*analysis
Sphingomonadaceae/genetics/isolation & purification/metabolism

@article {pmid31863999,
year = {2019},
author = {Llorens-Marès, T and Catalan, J and Casamayor, EO},
title = {Taxonomy and functional interactions in upper and bottom waters of an oligotrophic high-mountain deep lake (Redon, Pyrenees) unveiled by microbial metagenomics.},
journal = {The Science of the total environment},
volume = {707},
number = {},
pages = {135929},
doi = {10.1016/j.scitotenv.2019.135929},
pmid = {31863999},
issn = {1879-1026},
abstract = {High mountain lakes are, in general, highly sensitive systems to external forcing and good sentinels of global environmental changes. For a better understanding of internal lake processes, we examined microbial biodiversity and potential biogeochemical interactions in the oligotrophic deep high-mountain Lake Redon (Pyrenees, 2240 m altitude) using shotgun metagenomics. We analyzed the two ends of the range of environmental conditions found in Lake Redon, at 2 and 60 m depths. Bacteria were the most abundant component of the metagenomic reads (>90%) and the diversity indices of both taxonomic (16S and 18S rRNA) and functional (carbon-, nitrogen-, sulfur-, and phosphorous-cycling) related genes were higher in the bottom dark layer than in the upper compartment. A marked segregation was observed both in biodiversity and in the dominant energy and biomass generating pathways between the extremes. The aerobic respiration was mainly dominated by heterotrophic Burkholderiales at the top and Actinobacteria and Burkholderiales at the lake bottom. The potential for an active nitrogen cycle (nitrogen fixation, nitrification, nitrite oxidation, and nitrate reduction) was mainly found at 60 m, and potential for methanogenesis, anaerobic ammonia oxidation and dissimilatory sulfur pathways were only observed there. Some unexpected and mostly unseen energy and biomass pathways were found relevant for the biogeochemical cycling in lake Redon, i.e., those related to carbon monoxide oxidation and phosphonates processing. We provide a general scheme of the main biogeochemical processes that may operate in the sentinel deep Lake Redon. This framework may help for a better understanding of the whole lake metabolism.},
}

@article {pmid31856722,
year = {2019},
author = {Zupančič, J and Turk, M and Črnigoj, M and Ambrožič Avguštin, J and Gunde-Cimerman, N},
title = {The dishwasher rubber seal acts as a reservoir of bacteria in the home environment.},
journal = {BMC microbiology},
volume = {19},
number = {1},
pages = {300},
doi = {10.1186/s12866-019-1674-5},
pmid = {31856722},
issn = {1471-2180},
support = {382228-1/2013//Ministrstvo za visoko šolstvo, znanost in tehnologijo/ ; P1-0170//Javna Agencija za Raziskovalno Dejavnost RS/ ; },
abstract = {BACKGROUND: In modern lifestyles, people make their everyday tasks easier by using household appliances, for example dishwashers. Previous studies showed massive contamination of dishwasher rubber seals with fungi, thus bacterial community, able to survive under harsh conditions, remain undetermined.

METHODS: Bacteria that colonise the extreme environment of household dishwasher rubber seals were investigated using cultivation-dependent and metagenomic approaches. All bacterial isolates were tested for resistance to seven selected antibiotics. Same time bacterial diversity of tap water, connected to the dishwashers was investigated.

RESULTS: All 30 dishwashers investigated were colonised by various bacteria. Cultivation approaches resulted in 632 bacterial isolates in total, belonging to four phyla, eight classes, 40 genera and 74 species. The majority were Gram-positive, as solely Firmicutes (dominated by the Bacillus cereus group) and Actinobacteria. Gammaproteobacteria were primarily represented by Stenotrophomonas maltophilia, Pseudomonas aeruginosa and Escherichia coli. Metagenomic assessment of the bacterial biodiversity of the dishwasher rubber seals confirmed the predominance of Gram-positive bacteria, as primarily Actinobacteria, followed by Proteobacteria dominated by Gammaproteobacteria, and by pathogenic species such as Escherichia sp., Acinetobacter baumannii, Pseudomonas sp., Stenotrophomonas maltophilia, and Enterobacter sp.. Metagenomic assessment of bacterial biodiversity in the tap water connected to dishwashers revealed predominance of Gram-negative bacteria, in particular Proteobacteria, mainly represented by Tepidimonas sp.. Actinobacteria showed low numbers while no Firmicutes were detected in the tap water. The bacterial diversity of tap water was also lower, 23 genera compared to 39 genera on dishwasher rubber seals. Only 13 out of 49 genera identified by metagenomics approach was found in both environments, of those Gordonia was enriched while half of 13 genera were depleted in dishwashers compared to tap water.

CONCLUSIONS: These data indicate that colonisation of dishwasher rubber seals probably depends primarily on the bacterial input from the dirty vessels, and much less on the bacteria in the tap water. Based on the antibiotic resistance data, the dishwasher rubber seal bacterial isolates do not represent a serious threat for the spread of antibiotic resistance into the household environment. Nevertheless dishwashers cannot be ignored as potential sources of human infections, in particular for immuno-compromised individuals.},
}

@article {pmid31361989,
year = {2019},
author = {Abbasi, I and Nasereddin, A and Warburg, A},
title = {Development of a next generation DNA sequencing-based multi detection assay for detecting and identifying Leishmania parasites, blood sources, plant meals and intestinal microbiome in phlebotomine sand flies.},
journal = {Acta tropica},
volume = {199},
number = {},
pages = {105101},
doi = {10.1016/j.actatropica.2019.105101},
pmid = {31361989},
issn = {1873-6254},
mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Insect Vectors/*parasitology ; Leishmania/genetics/*isolation & purification ; Leishmaniasis/transmission ; Phlebotomus/*parasitology ; },
abstract = {Leishmaniasis is a disease caused by Leishmania parasites transmitted by phlebotomine sand flies (Diptera: Psychodidae). Human infections with different Leishmania species cause characteristic clinical manifestations; cutaneous or visceral leishmaniasis. Here we describe the development and application of a Miseq Next GenerationSequencing (NGS)-based Multi Detection Assay (MDA) designed to characterize metagenomics parameters pertinent to the sand fly vectors which may affect their vectorial capacity for Leishmania. For this purpose, we developed a MDA by which, DNA fragments were amplified through polymerase chain reactions (PCR) and then sequenced by MiSeq/NGS. PCR amplification was achieved using some published and some new primers designed specifically for identifying Leishmania spp. (ITS1), sand fly spp. (cytochrome oxidase I), vertebrate blood (Cytochrome b), plant DNA ribulose-1,5-bisphosphate carboxylase large subunit gene (rbcL), and prokaryotic micobiome (16 s rRNA). This MDA/NGS analysis was performed on two species of wild-caught sand flies that transmit different Leishmania spp. in two ecologically distinct, but geographically neighboring locations. The results were analyzed to identify, quantitate and correlate the measured parameters in order to assess their putative importance in the transmission dynamics of leishmaniasis.},
}

Animals
Female
*Gastrointestinal Microbiome
High-Throughput Nucleotide Sequencing/*methods
Humans
Insect Vectors/*parasitology
Leishmania/genetics/*isolation & purification
Leishmaniasis/transmission
Phlebotomus/*parasitology

@article {pmid31426820,
year = {2019},
author = {Li, H and Li, H and Wang, J and Guo, L and Fan, H and Zheng, H and Yang, Z and Huang, X and Chu, M and Yang, F and He, Z and Li, N and Yang, J and Wu, Q and Shi, H and Liu, L},
title = {The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites.},
journal = {Virology journal},
volume = {16},
number = {1},
pages = {105},
doi = {10.1186/s12985-019-1211-z},
pmid = {31426820},
issn = {1743-422X},
mesh = {Animals ; Anti-Bacterial Agents/administration & dosage ; Bacteria/classification/*isolation & purification ; Feces/microbiology/virology ; Gastrointestinal Microbiome/*drug effects ; Longitudinal Studies ; Macaca mulatta/microbiology/virology ; Metabolic Networks and Pathways ; Metabolome ; Metagenomics ; *Microbial Interactions ; Viruses/classification/*isolation & purification ; },
abstract = {BACKGROUND: The gut microbiome is closely associated with the health of the host; although the interaction between the bacterial microbiome and the whole virome has rarely been studied, it is likely of medical importance. Examination of the interactions between the gut bacterial microbiome and virome of rhesus monkey would significantly contribute to revealing the gut microbiome composition.

METHODS: Here, we conducted a metagenomic analysis of the gut microbiome of rhesus monkeys in a longitudinal cohort treated with an antibiotic cocktail, and we documented the interactions between the bacterial microbiome and virome. The depletion of viral populations was confirmed at the species level by real-time PCR. We also detected changes in the gut metabolome by GC-MS and LC-MS.

RESULTS: A majority of bacteria were depleted after treatment with antibiotics, and the Shannon diversity index decreased from 2.95 to 0.22. Furthermore, the abundance-based coverage estimator (ACE) decreased from 104.47 to 33.84, and the abundance of eukaryotic viruses also changed substantially. In the annotation, 6 families of DNA viruses and 1 bacteriophage family were present in the normal monkeys but absent after gut bacterial microbiome depletion. Intriguingly, we discovered that changes in the gut bacterial microbiome composition may promote changes in the gut virome composition, and tryptophan, arginine, and quinone may play roles in the interaction between the bacterial microbiome and virome.

CONCLUSION: Our results indicated that the clearly altered composition of the virome was correlated with depletion in the bacterial community and that metabolites produced by bacteria possibly play important roles in the interaction.},
}

Animals
Anti-Bacterial Agents/administration & dosage
Bacteria/classification/*isolation & purification
Feces/microbiology/virology
Gastrointestinal Microbiome/*drug effects
Longitudinal Studies
Macaca mulatta/microbiology/virology
Metabolic Networks and Pathways
Metabolome
Metagenomics
*Microbial Interactions
Viruses/classification/*isolation & purification

@article {pmid31415755,
year = {2019},
author = {Tierney, BT and Yang, Z and Luber, JM and Beaudin, M and Wibowo, MC and Baek, C and Mehlenbacher, E and Patel, CJ and Kostic, AD},
title = {The Landscape of Genetic Content in the Gut and Oral Human Microbiome.},
journal = {Cell host & microbe},
volume = {26},
number = {2},
pages = {283-295.e8},
doi = {10.1016/j.chom.2019.07.008},
pmid = {31415755},
issn = {1934-6069},
support = {R00 ES023504/ES/NIEHS NIH HHS/United States ; R01 AI127250/AI/NIAID NIH HHS/United States ; R21 ES025052/ES/NIEHS NIH HHS/United States ; P30 DK036836/DK/NIDDK NIH HHS/United States ; T32 DK110919/DK/NIDDK NIH HHS/United States ; K99 ES023504/ES/NIEHS NIH HHS/United States ; },
mesh = {Bacteria/classification/genetics ; Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; Databases, Factual ; Gastrointestinal Tract/microbiology ; Genetic Heterogeneity ; Host Microbial Interactions ; Humans ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics/*physiology ; Mouth/microbiology ; Multigene Family ; Phenotype ; },
abstract = {Despite substantial interest in the species diversity of the human microbiome and its role in disease, the scale of its genetic diversity, which is fundamental to deciphering human-microbe interactions, has not been quantified. Here, we conducted a cross-study meta-analysis of metagenomes from two human body niches, the mouth and gut, covering 3,655 samples from 13 studies. We found staggering genetic heterogeneity in the dataset, identifying a total of 45,666,334 non-redundant genes (23,961,508 oral and 22,254,436 gut) at the 95% identity level. Fifty percent of all genes were "singletons," or unique to a single metagenomic sample. Singletons were enriched for different functions (compared with non-singletons) and arose from sub-population-specific microbial strains. Overall, these results provide potential bases for the unexplained heterogeneity observed in microbiome-derived human phenotypes. One the basis of these data, we built a resource, which can be accessed at https://microbial-genes.bio.},
}

Bacteria/classification/genetics
Biodiversity
Cluster Analysis
DNA Fingerprinting
Databases, Factual
Gastrointestinal Tract/microbiology
Genetic Heterogeneity
Host Microbial Interactions
Humans
Metagenome/*genetics
Metagenomics
Microbiota/*genetics/*physiology
Mouth/microbiology
Multigene Family
Phenotype

@article {pmid31399369,
year = {2019},
author = {Thingholm, LB and Rühlemann, MC and Koch, M and Fuqua, B and Laucke, G and Boehm, R and Bang, C and Franzosa, EA and Hübenthal, M and Rahnavard, A and Frost, F and Lloyd-Price, J and Schirmer, M and Lusis, AJ and Vulpe, CD and Lerch, MM and Homuth, G and Kacprowski, T and Schmidt, CO and Nöthlings, U and Karlsen, TH and Lieb, W and Laudes, M and Franke, A and Huttenhower, C},
title = {Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition.},
journal = {Cell host & microbe},
volume = {26},
number = {2},
pages = {252-264.e10},
doi = {10.1016/j.chom.2019.07.004},
pmid = {31399369},
issn = {1934-6069},
support = {T32 HL069766/HL/NHLBI NIH HHS/United States ; P01 HL028481/HL/NHLBI NIH HHS/United States ; R01 HL144651/HL/NHLBI NIH HHS/United States ; R01 GM083198/GM/NIGMS NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Diabetes Mellitus, Type 2/*complications ; Diet ; Dietary Supplements ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Germany ; Humans ; Iron/metabolism ; Magnesium/metabolism ; Male ; Metabolic Diseases/complications ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Multivariate Analysis ; Nutrition Assessment ; Obesity/*complications/*microbiology ; Serum/metabolism ; },
abstract = {Obesity and type 2 diabetes (T2D) are metabolic disorders that are linked to microbiome alterations. However, their co-occurrence poses challenges in disentangling microbial features unique to each condition. We analyzed gut microbiomes of lean non-diabetic (n = 633), obese non-diabetic (n = 494), and obese individuals with T2D (n = 153) from German population and metabolic disease cohorts. Microbial taxonomic and functional profiles were analyzed along with medical histories, serum metabolomics, biometrics, and dietary data. Obesity was associated with alterations in microbiome composition, individual taxa, and functions with notable changes in Akkermansia, Faecalibacterium, Oscillibacter, and Alistipes, as well as in serum metabolites that correlated with gut microbial patterns. However, microbiome associations were modest for T2D, with nominal increases in Escherichia/Shigella. Medications, including antihypertensives and antidiabetics, along with dietary supplements including iron, were significantly associated with microbiome variation. These results differentiate microbial components of these interrelated metabolic diseases and identify dietary and medication exposures to consider in future studies.},
}

Animals
Bacteria/classification/genetics/isolation & purification
Biodiversity
Diabetes Mellitus, Type 2/*complications
Diet
Dietary Supplements
Feces/microbiology
Female
Gastrointestinal Microbiome/*physiology
Germany
Humans
Iron/metabolism
Magnesium/metabolism
Male
Metabolic Diseases/complications
Metagenomics
Mice
Mice, Inbred C57BL
Multivariate Analysis
Nutrition Assessment
Obesity/*complications/*microbiology
Serum/metabolism

@article {pmid30562162,
year = {2018},
author = {Peng, W and Yi, P and Yang, J and Xu, P and Wang, Y and Zhang, Z and Huang, S and Wang, Z and Zhang, C},
title = {Association of gut microbiota composition and function with a senescence-accelerated mouse model of Alzheimer's Disease using 16S rRNA gene and metagenomic sequencing analysis.},
journal = {Aging},
volume = {10},
number = {12},
pages = {4054-4065},
doi = {10.18632/aging.101693},
pmid = {30562162},
issn = {1945-4589},
mesh = {Aging ; Alzheimer Disease ; Animals ; *Disease Models, Animal ; Gastrointestinal Microbiome/*genetics ; Male ; Metagenomics ; Mice ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Although an intriguing potential association of the gut microbiome with Alzheimer's disease (AD) has attracted recent interest, few studies have directly assessed this relationship or underlying mechanism. Here, we compared the gut microbiota composition and functional differentiation of senescence-accelerated mouse prone 8 (SAMP8) mice with control senescence-accelerated mouse resistant 1 (SAMR1) mice using 16S rRNA gene and metagenomic sequencing analysis, respectively. Specifically, 16S sequencing results showed that the SAMP8 mice displayed a characteristic composition of the gut microbiome that clearly differed from that of the SAMR1 mice. Moreover, network analysis revealed that the gut microbiota of SAMP8 mice had decreased correlation density and clustering of operational taxonomic units. Metagenomic results revealed that the predominant Cluster of Orthologous Groups functional category related to these changes was the metabolism cluster in SAMP8 mice. The Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation further demonstrated enrichment of the relative abundance of some dominant metabolism-related KEGG pathways in the SAMP8 mice, consistent with the suggested pathogenic mechanisms of AD. In conclusion, this study suggests that perturbations of the gut microbiota composition and the functional metagenome may be associated with AD. Further studies are warranted to elucidate the potential new mechanism contributing to AD progression.},
}

Aging
Alzheimer Disease
Animals
*Disease Models, Animal
Gastrointestinal Microbiome/*genetics
Male
Metagenomics
Mice
RNA, Bacterial/*genetics
RNA, Ribosomal, 16S/*genetics

@article {pmid30406643,
year = {2019},
author = {Gao, B and Chi, L and Tu, P and Gao, N and Lu, K},
title = {The Carbamate Aldicarb Altered the Gut Microbiome, Metabolome, and Lipidome of C57BL/6J Mice.},
journal = {Chemical research in toxicology},
volume = {32},
number = {1},
pages = {67-79},
doi = {10.1021/acs.chemrestox.8b00179},
pmid = {30406643},
issn = {1520-5010},
support = {R01 ES024950/ES/NIEHS NIH HHS/United States ; },
mesh = {Administration, Oral ; Aldicarb/administration & dosage/*pharmacology ; Animals ; DNA Damage ; Gastrointestinal Microbiome/*drug effects ; Insecticides/administration & dosage/*pharmacology ; Lipidomics ; *Lipids ; Male ; Metabolome/*drug effects ; Mice ; Mice, Inbred C57BL ; Molecular Structure ; Oxidative Stress/drug effects ; },
abstract = {The gut microbiome is highly involved in numerous aspects of host physiology, from energy harvest to stress response, and can confer many benefits to the host. The gut microbiome development could be affected by genetic and environmental factors, including pesticides. The carbamate insecticide aldicarb has been extensively used in agriculture, which raises serious public health concerns. However, the impact of aldicarb on the gut microbiome, host metabolome, and lipidome has not been well studied yet. Herein, we use multiomics approaches, including16S rRNA sequencing, shotgun metagenomics sequencing, metabolomics, and lipidomics, to elucidate aldicarb-induced toxicity in the gut microbiome and the host metabolic homeostasis. We demonstrated that aldicarb perturbed the gut microbiome development trajectory, enhanced gut bacterial pathogenicity, altered complex lipid profile, and induced oxidative stress, protein degradation, and DNA damage. The brain metabolism was also disturbed by the aldicarb exposure. These findings may provide a novel understanding of the toxicity of carbamate insecticides.},
}

Administration, Oral
Aldicarb/administration & dosage/*pharmacology
Animals
DNA Damage
Gastrointestinal Microbiome/*drug effects
Insecticides/administration & dosage/*pharmacology
Lipidomics
*Lipids
Male
Metabolome/*drug effects
Mice
Mice, Inbred C57BL
Molecular Structure
Oxidative Stress/drug effects

@article {pmid31849864,
year = {2019},
author = {Bains, M and Laney, C and Wolfe, AE and Orr, M and Waschek, JA and Ericsson, AC and Dorsam, GP},
title = {Vasoactive Intestinal Peptide Deficiency Is Associated With Altered Gut Microbiota Communities in Male and Female C57BL/6 Mice.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2689},
doi = {10.3389/fmicb.2019.02689},
pmid = {31849864},
issn = {1664-302X},
abstract = {Vasoactive intestinal peptide (VIP) is crucial for gastrointestinal tract (GIT) health. VIP sustains GIT homeostasis through maintenance of the intestinal epithelial barrier and acts as a potent anti-inflammatory mediator that contributes to gut bacterial tolerance. Based on these biological functions by VIP, we hypothesized that its deficiency would alter gut microbial ecology. To this end, fecal samples from male and female VIP+/+, VIP+/-, and VIP-/- littermates (n = 47) were collected and 16S rRNA sequencing was conducted. Our data revealed significant changes in bacterial composition, biodiversity, and weight loss from VIP-/- mice compared to VIP+/+ and VIP+/- littermates, irrespective of sex. The gut bacteria compositional changes observed in VIP-/- mice was consistent with gut microbial structure changes reported for certain inflammatory and autoimmune disorders. Moreover, predicted functional changes by PICRUSt software suggested an energy surplus within the altered microbiota from VIP-/- mice. These data support that VIP plays an important role in maintaining microbiota balance, biodiversity, and GIT function, and its genetic removal results in significant gut microbiota restructuring and weight loss.},
}

@article {pmid31429791,
year = {2019},
author = {Casimiro-Soriguer, CS and Loucera, C and Perez Florido, J and López-López, D and Dopazo, J},
title = {Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples.},
journal = {Biology direct},
volume = {14},
number = {1},
pages = {15},
doi = {10.1186/s13062-019-0246-9},
pmid = {31429791},
issn = {1745-6150},
mesh = {Biomarkers/*analysis ; Cities ; *Drug Resistance, Microbial ; *Machine Learning ; *Metabolome ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; },
abstract = {BACKGROUND: The availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies involve the analysis of bacterial abundance profiles.

RESULTS: Here we use a transformation of the conventional bacterial strain or gene abundance profiles to functional profiles that account for bacterial metabolism and other cell functionalities. These profiles are used as features for city classification in a machine learning algorithm that allows the extraction of the most relevant features for the classification.

CONCLUSIONS: We demonstrate here that the use of functional profiles not only predict accurately the most likely origin of a sample but also to provide an interesting functional point of view of the biogeography of the microbiota. Interestingly, we show how cities can be classified based on the observed profile of antibiotic resistances.

REVIEWERS: Open peer review: Reviewed by Jin Zhuang Dou, Jing Zhou, Torsten Semmler and Eran Elhaik.},
}

Biomarkers/*analysis
Cities
*Drug Resistance, Microbial
*Machine Learning
*Metabolome
*Metagenome
Metagenomics/*methods
Microbiota/*genetics

@article {pmid31420049,
year = {2019},
author = {Ryan, FJ},
title = {Application of machine learning techniques for creating urban microbial fingerprints.},
journal = {Biology direct},
volume = {14},
number = {1},
pages = {13},
doi = {10.1186/s13062-019-0245-x},
pmid = {31420049},
issn = {1745-6150},
mesh = {Cities ; DNA Fingerprinting/*methods ; *Machine Learning ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; },
abstract = {BACKGROUND: Research has found that human associated microbial communities play a role in homeostasis and the disruption of these communities may be important in an array of medical conditions. However outside of the human body many of these communities remain poorly studied. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is characterizing the microbiomes of urban environments with the aim to improve design of mass transit systems. As part of the CAMDA 2018 MetaSUB Forensics Challenge 311 city microbiome samples were provided to create urban microbial fingerprints, as well as a further 3 mystery datasets for validation.

RESULTS: MetaSUB samples were clustered using t-SNE in an unsupervised fashion to almost discrete groups, which upon inspection represented city of origin. Based on this clustering, geographically close metropolitan areas appear to display similar microbial profiles such as those of Auckland and Hamilton. Mystery unlabeled samples were provided part of the challenge. A random forest classifier built on the initial dataset of 311 samples was capable of correctly classifying 83.3% of the mystery samples to their city of origin. Random Forest analyses also identified features with the highest discriminatory power, ranking bacterial species such as Campylobacter jejuni and Staphylococcus argenteus as highly predictive of city of origin. The surface from which the sample was collected displayed little detectable impact on the microbial profiles in the data generated here. The proportion of reads classified per sample varied greatly and so de-novo assembly was applied to recover genomic fragments representing organisms not captured in reference databases.

CONCLUSIONS: Current methods can differentiate urban microbiome profiles from each other with relative ease. De-novo assembly indicated that the MetaSUB metagenomic data contains adequate depth to recover metagenomic assembled genomes and that current databases are not sufficient to fully characterize urban microbiomes. Profiles found here indicate there may be a relationship between geographical distance between areas and the urban microbiome composition although this will need further research. The impact of these different profiles on public health is currently unknown but the MetaSUB consortium is uniquely suited to evaluate these and provide a roadmap for the inclusion of urban microbiome information for city planning and public health policy.

REVIEWERS: This article was reviewed by Dimitar Vassilev, Eran Elhaik and Chengsheng Zhu.},
}

Cities
DNA Fingerprinting/*methods
*Machine Learning
Metagenome/*genetics
Metagenomics/*methods
Microbiota/*genetics

@article {pmid31400683,
year = {2019},
author = {Ceccon, DM and Faoro, H and Lana, PDC and Souza, EM and Pedrosa, FO},
title = {Metataxonomic and metagenomic analysis of mangrove microbiomes reveals community patterns driven by salinity and pH gradients in Paranaguá Bay, Brazil.},
journal = {The Science of the total environment},
volume = {694},
number = {},
pages = {133609},
doi = {10.1016/j.scitotenv.2019.133609},
pmid = {31400683},
issn = {1879-1026},
mesh = {Bays/chemistry/*microbiology ; Brazil ; *Environmental Monitoring ; Hydrogen-Ion Concentration ; *Metagenomics ; *Microbiota ; *Salinity ; },
abstract = {While environmental drivers regulate the structure of mangrove microbial communities, their exact nature and the extent of their influence require further elucidation. By means of 16S rRNA gene-based sequencing, we determined the microbial taxonomic profiles of mangroves in the subtropical Paranaguá Bay, Brazil, considering as potential drivers: salinity, as represented by two sectors in the extremes of a salinity gradient (<5 PSU and >30 PSU); proximity to/absence of the prevailing plants, Avicennia schaueriana, Laguncularia racemosa, Rhizophora mangle, and Spartina alterniflora; and the chemical composition of the sediments. Salinity levels within the estuary had the strongest influence on microbial structure, and pH was important to separate two communities within the high salinity environment. About one fourth of the total variation in community structure resulted from covariation of salinity and the overall chemical composition, which might indicate that the chemical profile was also related to salinity. The most prevalent bacterial phyla associated with the mangrove soils analyzed included Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Cyanobacteria. Taxonomic and functional comparisons of our results for whole-genome sequencing with available data from other biomes showed that the studied microbiomes cluster first according to biome type, then to matrix type and salinity status. Metabolic functions were more conserved than organisms within mangroves and across all biomes, indicating that core functions are preserved in any of the given conditions regardless of the specific organisms harboring them.},
}

Bays/chemistry/*microbiology
Brazil
*Environmental Monitoring
Hydrogen-Ion Concentration
*Metagenomics
*Microbiota
*Salinity

@article {pmid31371723,
year = {2019},
author = {Coyne, MJ and Béchon, N and Matano, LM and McEneany, VL and Chatzidaki-Livanis, M and Comstock, LE},
title = {A family of anti-Bacteroidales peptide toxins wide-spread in the human gut microbiota.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {3460},
doi = {10.1038/s41467-019-11494-1},
pmid = {31371723},
issn = {2041-1723},
support = {P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 AI093771/AI/NIAID NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/*biosynthesis/pharmacology ; Bacterial Proteins/biosynthesis/genetics/pharmacology ; Bacterial Toxins/*biosynthesis/genetics/pharmacology ; Bacteriocins/*biosynthesis/*genetics/pharmacology ; Bacteroidetes/drug effects/genetics/*metabolism ; Base Sequence ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal/genetics ; Humans ; Interspersed Repetitive Sequences ; Metagenomics ; Microbial Sensitivity Tests ; Peptides/genetics/*metabolism/pharmacology ; Prevotella/drug effects ; Sequence Analysis, Protein ; Vaginosis, Bacterial ; },
abstract = {Bacteria often produce antimicrobial toxins to compete in microbial communities. Here we identify a family of broad-spectrum peptide toxins, named bacteroidetocins, produced by Bacteroidetes species. We study this toxin family using phenotypic, mutational, bioinformatic, and human metagenomic analyses. Bacteroidetocins are related to class IIa bacteriocins of Gram-positive bacteria and kill members of the Bacteroidetes phylum, including Bacteroides, Parabacteroides, and Prevotella gut species, as well as pathogenic Prevotella species. The bacteroidetocin biosynthesis genes are found in horizontally acquired mobile elements, which likely allow dissemination within the gut microbiota and may explain their wide distribution in human populations. Bacteroidetocins may have potential applications in microbiome engineering and as therapeutics for polymicrobial diseases such as bacterial vaginosis and periodontal disease.},
}

Anti-Bacterial Agents/*biosynthesis/pharmacology
Bacterial Proteins/biosynthesis/genetics/pharmacology
Bacterial Toxins/*biosynthesis/genetics/pharmacology
Bacteriocins/*biosynthesis/*genetics/pharmacology
Bacteroidetes/drug effects/genetics/*metabolism
Base Sequence
Female
Gastrointestinal Microbiome/genetics/*physiology
Gastrointestinal Tract/microbiology
Gene Transfer, Horizontal/genetics
Humans
Interspersed Repetitive Sequences
Metagenomics
Microbial Sensitivity Tests
Peptides/genetics/*metabolism/pharmacology
Prevotella/drug effects
Sequence Analysis, Protein
Vaginosis, Bacterial

@article {pmid31370905,
year = {2019},
author = {Harris, ZN and Dhungel, E and Mosior, M and Ahn, TH},
title = {Massive metagenomic data analysis using abundance-based machine learning.},
journal = {Biology direct},
volume = {14},
number = {1},
pages = {12},
doi = {10.1186/s13062-019-0242-0},
pmid = {31370905},
issn = {1745-6150},
mesh = {*Data Analysis ; *Machine Learning ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; },
abstract = {BACKGROUND: Metagenomics is the application of modern genomic techniques to investigate the members of a microbial community directly in their natural environments and is widely used in many studies to survey the communities of microbial organisms that live in diverse ecosystems. In order to understand the metagenomic profile of one of the densest interaction spaces for millions of people, the public transit system, the MetaSUB international Consortium has collected and sequenced metagenomes from subways of different cities across the world. In collaboration with CAMDA, MetaSUB has made the metagenomic samples from these cities available for an open challenge of data analysis including, but not limited in scope to, the identification of unknown samples.

RESULTS: To distinguish the metagenomic profiling among different cities and also predict unknown samples precisely based on the profiling, two different approaches are proposed using machine learning techniques; one is a read-based taxonomy profiling of each sample and prediction method, and the other is a reduced representation assembly-based method. Among various machine learning techniques tested, the random forest technique showed promising results as a suitable classifier for both approaches. Random forest models developed from read-based taxonomic profiling could achieve an accuracy of 91% with 95% confidence interval between 80 and 93%. The assembly-based random forest model prediction also reached 90% accuracy. However, both models achieved roughly the same accuracy on the testing test, whereby they both failed to predict the most abundant label.

CONCLUSION: Our results suggest that both read-based and assembly-based approaches are powerful tools for the analysis of metagenomics data. Moreover, our results suggest that reduced representation assembly-based methods are able to simultaneous provide high-accuracy prediction on available data. Overall, we show that metagenomic samples can be traced back to their location with careful generation of features from the composition of microbes and utilizing existing machine learning algorithms. Proposed approaches show high accuracy of prediction, but require careful inspection before making any decisions due to sample noise or complexity.

REVIEWERS: This article was reviewed by Eugene V. Koonin, Jing Zhou and Serghei Mangul.},
}

*Data Analysis
*Machine Learning
*Metagenome
Metagenomics/*methods
Microbiota/*genetics

@article {pmid31340852,
year = {2019},
author = {Walker, AR and Datta, S},
title = {Identification of city specific important bacterial signature for the MetaSUB CAMDA challenge microbiome data.},
journal = {Biology direct},
volume = {14},
number = {1},
pages = {11},
doi = {10.1186/s13062-019-0243-z},
pmid = {31340852},
issn = {1745-6150},
mesh = {Bacteria/*genetics ; Cities ; High-Throughput Nucleotide Sequencing/*methods ; *Machine Learning ; Metagenomics/*methods ; Microbiota/*genetics ; },
abstract = {BACKGROUND: Metagenomic data of whole genome sequences (WGS) from samples across several cities around the globe may unravel city specific signatures of microbes. Illumina MiSeq sequencing data was provided from 12 cities in 7 different countries as part of the 2018 CAMDA "MetaSUB Forensic Challenge", including also samples from three mystery sets. We used appropriate machine learning techniques on this massive dataset to effectively identify the geographical provenance of "mystery" samples. Additionally, we pursued compositional data analysis to develop accurate inferential techniques for such microbiome data. It is expected that this current data, which is of higher quality and higher sequence depth compared to the CAMDA 2017 MetaSUB challenge data, along with improved analytical techniques would yield many more interesting, robust and useful results that can be beneficial for forensic analysis.

RESULTS: A preliminary quality screening of the data revealed a much better dataset in terms of Phred quality score (hereafter Phred score), and larger paired-end MiSeq reads, and a more balanced experimental design, though still not equal number of samples across cities. PCA (Principal Component Analysis) analysis showed interesting clusters of samples and a large amount of the variability in the data was explained by the first three components (~ 70%). The classification analysis proved to be consistent across both the testing mystery sets with a similar percentage of the samples correctly predicted (up to 90%). The analysis of the relative abundance of bacterial "species" showed that some "species" are specific to some regions and can play important roles for predictions. These results were also corroborated by the variable importance given to the "species" during the internal cross validation (CV) run with Random Forest (RF).

CONCLUSIONS: The unsupervised analysis (PCA and two-way heatmaps) of the log2-cpm normalized data and relative abundance differential analysis seemed to suggest that the bacterial signature of common "species" was distinctive across the cities; which was also supported by the variable importance results. The prediction of the city for mystery sets 1 and 3 showed convincing results with high classification accuracy/consistency. The focus of this work on the current MetaSUB data and the analytical tools utilized here can be of great help in forensic, metagenomics, and other sciences to predict city of provenance of metagenomic samples, as well as in other related fields. Additionally, the pairwise analysis of relative abundance showed that the approach provided consistent and comparable "species" when compared with the classification importance variables.

REVIEWERS: This article was reviewed by Manuela Oliveira, Dimitar Vassilev, and Patrick Lee.},
}

Bacteria/*genetics
Cities
High-Throughput Nucleotide Sequencing/*methods
*Machine Learning
Metagenomics/*methods
Microbiota/*genetics

@article {pmid31332169,
year = {2019},
author = {Antunes, KH and Fachi, JL and de Paula, R and da Silva, EF and Pral, LP and Dos Santos, AÁ and Dias, GBM and Vargas, JE and Puga, R and Mayer, FQ and Maito, F and Zárate-Bladés, CR and Ajami, NJ and Sant'Ana, MR and Candreva, T and Rodrigues, HG and Schmiele, M and Silva Clerici, MTP and Proença-Modena, JL and Vieira, AT and Mackay, CR and Mansur, D and Caballero, MT and Marzec, J and Li, J and Wang, X and Bell, D and Polack, FP and Kleeberger, SR and Stein, RT and Vinolo, MAR and de Souza, APD},
title = {Microbiota-derived acetate protects against respiratory syncytial virus infection through a GPR43-type 1 interferon response.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {3273},
doi = {10.1038/s41467-019-11152-6},
pmid = {31332169},
issn = {2041-1723},
mesh = {A549 Cells ; Acetates/metabolism/*pharmacology ; Animals ; Cell Line ; Chlorocebus aethiops ; Humans ; Interferon Type I/*metabolism ; Lung/drug effects/metabolism/virology ; Mice, Inbred C57BL ; Mice, Knockout ; *Microbiota ; Polymorphism, Single Nucleotide ; Protective Agents/metabolism/pharmacology ; Receptor, Interferon alpha-beta/genetics ; Receptors, G-Protein-Coupled/genetics/*metabolism ; Respiratory Syncytial Virus Infections/genetics/*prevention & control/virology ; Vero Cells ; Viral Load/drug effects/genetics ; },
abstract = {Severe respiratory syncytial virus (RSV) infection is a major cause of morbidity and mortality in infants <2 years-old. Here we describe that high-fiber diet protects mice from RSV infection. This effect was dependent on intestinal microbiota and production of acetate. Oral administration of acetate mediated interferon-β (IFN-β) response by increasing expression of interferon-stimulated genes in the lung. These effects were associated with reduction of viral load and pulmonary inflammation in RSV-infected mice. Type 1 IFN signaling via the IFN-1 receptor (IFNAR) was essential for acetate antiviral activity in pulmonary epithelial cell lines and for the acetate protective effect in RSV-infected mice. Activation of Gpr43 in pulmonary epithelial cells reduced virus-induced cytotoxicity and promoted antiviral effects through IFN-β response. The effect of acetate on RSV infection was abolished in Gpr43-/- mice. Our findings reveal antiviral effects of acetate involving IFN-β in lung epithelial cells and engagement of GPR43 and IFNAR.},
}

A549 Cells
Acetates/metabolism/*pharmacology
Animals
Cell Line
Chlorocebus aethiops
Humans
Interferon Type I/*metabolism
Lung/drug effects/metabolism/virology
Mice, Inbred C57BL
Mice, Knockout
*Microbiota
Polymorphism, Single Nucleotide
Protective Agents/metabolism/pharmacology
Receptor, Interferon alpha-beta/genetics
Receptors, G-Protein-Coupled/genetics/*metabolism
Respiratory Syncytial Virus Infections/genetics/*prevention & control/virology
Vero Cells
Viral Load/drug effects/genetics

@article {pmid31250899,
year = {2019},
author = {Aluthge, ND and Van Sambeek, DM and Carney-Hinkle, EE and Li, YS and Fernando, SC and Burkey, TE},
title = {BOARD INVITED REVIEW: The pig microbiota and the potential for harnessing the power of the microbiome to improve growth and health1.},
journal = {Journal of animal science},
volume = {97},
number = {9},
pages = {3741-3757},
doi = {10.1093/jas/skz208},
pmid = {31250899},
issn = {1525-3163},
mesh = {Animals ; Diet/veterinary ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Metabolomics ; *Prebiotics ; *Probiotics ; Swine/growth & development/*microbiology/physiology ; *Synbiotics ; },
abstract = {A variety of microorganisms inhabit the gastrointestinal tract of animals including bacteria, archaea, fungi, protozoa, and viruses. Pioneers in gut microbiology have stressed the critical importance of diet:microbe interactions and how these interactions may contribute to health status. As scientists have overcome the limitations of culture-based microbiology, the importance of these interactions has become more clear even to the extent that the gut microbiota has emerged as an important immunologic and metabolic organ. Recent advances in metagenomics and metabolomics have helped scientists to demonstrate that interactions among the diet, the gut microbiota, and the host to have profound effects on animal health and disease. However, although scientists have now accumulated a great deal of data with respect to what organisms comprise the gastrointestinal landscape, there is a need to look more closely at causative effects of the microbiome. The objective of this review is intended to provide: 1) a review of what is currently known with respect to the dynamics of microbial colonization of the porcine gastrointestinal tract; 2) a review of the impact of nutrient:microbe effects on growth and health; 3) examples of the therapeutic potential of prebiotics, probiotics, and synbiotics; and 4) a discussion about what the future holds with respect to microbiome research opportunities and challenges. Taken together, by considering what is currently known in the four aforementioned areas, our overarching goal is to set the stage for narrowing the path towards discovering how the porcine gut microbiota (individually and collectively) may affect specific host phenotypes.},
}

Animals
Diet/veterinary
*Gastrointestinal Microbiome
Gastrointestinal Tract/microbiology
Metabolomics
*Prebiotics
*Probiotics
Swine/growth & development/*microbiology/physiology
*Synbiotics

@article {pmid31247969,
year = {2019},
author = {Yu, JC and Hale, VL and Khodadadi, H and Baban, B},
title = {Whole Body Vibration-Induced Omental Macrophage Polarization and Fecal Microbiome Modification in a Murine Model.},
journal = {International journal of molecular sciences},
volume = {20},
number = {13},
pages = {},
doi = {10.3390/ijms20133125},
pmid = {31247969},
issn = {1422-0067},
mesh = {Animals ; Biodiversity ; Biomarkers ; Diabetes Mellitus, Type 2 ; Disease Models, Animal ; Feces/microbiology ; *Gastrointestinal Microbiome ; Immunophenotyping ; Macrophage Activation/*immunology ; Macrophages/*immunology/metabolism ; Metagenome ; Metagenomics/methods ; Mice ; Omentum/*immunology ; *Vibration ; },
abstract = {Human nutrient metabolism, developed millions of years ago, is anachronistic. Adaptive features that offered survival advantages are now great liabilities. The current dietary pattern, coupled with massively reduced physical activities, causes an epidemic of obesity and chronic metabolic diseases, such as type 2 diabetes mellitus. Chronic inflammation is a major contributing factor to the initiation and progression of most metabolic and cardiovascular diseases. Among all components of an innate immune system, due to their dual roles as phagocytic as well as antigen-presenting cells, macrophages play an important role in the regulation of inflammatory responses, affecting the body's microenvironment and homeostasis. Earlier studies have established the beneficial, anti-inflammatory effects of whole body vibration (WBV) as a partial exercise mimetic, including reversing the effects of glucose intolerance and hepatic steatosis. Here for the first time, we describe potential mechanisms by which WBV may improve metabolic status and ameliorate the adverse consequences through macrophage polarization and altering the fecal microbiome.},
}

Animals
Biodiversity
Biomarkers
Diabetes Mellitus, Type 2
Disease Models, Animal
Feces/microbiology
*Gastrointestinal Microbiome
Immunophenotyping
Macrophage Activation/*immunology
Macrophages/*immunology/metabolism
Metagenome
Metagenomics/methods
Mice
Omentum/*immunology
*Vibration

@article {pmid31242612,
year = {2019},
author = {Rampelotto, PH and Sereia, AFR and de Oliveira, LFV and Margis, R},
title = {Exploring the Hospital Microbiome by High-Resolution 16S rRNA Profiling.},
journal = {International journal of molecular sciences},
volume = {20},
number = {12},
pages = {},
doi = {10.3390/ijms20123099},
pmid = {31242612},
issn = {1422-0067},
mesh = {Bacteria/classification/genetics ; Biodiversity ; *Environmental Microbiology ; *Hospitals ; *Metagenomics/methods ; Microbiota/*genetics ; Models, Theoretical ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {The aim of this work was to analyze and compare the bacterial communities of 663 samples from a Brazilian hospital by using high-throughput sequencing of the 16S rRNA gene. To increase taxonomic profiling and specificity of 16S-based identification, a strict sequence quality filtering process was applied for the accurate identification of clinically relevant bacterial taxa. Our results indicate that the hospital environment is predominantly inhabited by closely related species. A massive dominance of a few taxa in all taxonomic levels down to the genera was observed, where the ten most abundant genera in each facility represented 64.4% of all observed taxa, with a major predominance of Acinetobacter and Pseudomonas. The presence of several nosocomial pathogens was revealed. Co-occurrence analysis indicated that the present hospital microbial network had low connectedness, forming a clustered topology, but not structured among groups of nodes (i.e., modules). Furthermore, we were able to detect ecologically relevant relationships between specific microbial taxa, in particular, potential competition between pathogens and non-pathogens. Overall, these results provide new insight into different aspects of a hospital microbiome and indicate that 16S rRNA sequencing may serve as a robust one-step tool for microbiological identification and characterization of a wide range of clinically relevant bacterial taxa in hospital settings with a high resolution.},
}

Bacteria/classification/genetics
Biodiversity
*Environmental Microbiology
*Hospitals
*Metagenomics/methods
Microbiota/*genetics
Models, Theoretical
RNA, Ribosomal, 16S/*genetics

@article {pmid31240226,
year = {2019},
author = {Yu, H and Qin, L and Hu, H and Wang, Z},
title = {Alteration of the Gut Microbiota and Its Effect on AMPK/NADPH Oxidase Signaling Pathway in 2K1C Rats.},
journal = {BioMed research international},
volume = {2019},
number = {},
pages = {8250619},
doi = {10.1155/2019/8250619},
pmid = {31240226},
issn = {2314-6141},
mesh = {AMP-Activated Protein Kinases/*metabolism ; Acetyl-CoA Carboxylase/metabolism ; Animals ; Bacteria/classification/metabolism ; Fatty Acids, Volatile/blood ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Kidney/*metabolism ; Male ; Metagenomics ; Models, Animal ; NADPH Oxidases/*metabolism ; Nitrates/blood ; Nitrites/blood ; Phosphorylation ; Rats ; Rats, Wistar ; Signal Transduction/*physiology ; Superoxide Dismutase/metabolism ; },
abstract = {Background: The purpose of this study was to evaluate the alteration of the gut microbiota and its effect on adenosine monophosphate-activated protein kinase (AMPK)/nicotinamide adenine dinucleotide phosphate oxidase (NADPH oxidase) signaling pathway in two-kidney one-clip (2K1C) rats.

Methods: The 2K1C rat models were established. The rats were randomly divided into the following 2 groups: 2K1C group and sham group. Alterations of the gut microbiota were analyzed based on the high throughput sequencing method. Plasma concentrations of short chain fatty acids (SCFAs) were measured by chromatography. The protein expression of phosphorylated AMPK and acetyl-CoA carboxylase (ACC) was determined by western blotting. NADPH oxidase activity was measured by a luminometer.

Results: Microbial community analyses revealed that the structure and composition of the gut microbiota were significantly disrupted in 2K1C rats when compared to sham rats. This disruption was associated with the drastic increase in relative abundance of the genera Prevotella and the decrease in SCFA-producing bacterial population. We further confirm that SCFAs produced by the gut microbiota influence NADPH oxidase activity through AMPK.

Conclusions: Our data implicated the important role of gut microbiota in the regulation of AMPK/NADPH oxidase signaling pathway.},
}

AMP-Activated Protein Kinases/*metabolism
Acetyl-CoA Carboxylase/metabolism
Animals
Bacteria/classification/metabolism
Fatty Acids, Volatile/blood
Feces/microbiology
Gastrointestinal Microbiome/*physiology
Humans
Kidney/*metabolism
Male
Metagenomics
Models, Animal
NADPH Oxidases/*metabolism
Nitrates/blood
Nitrites/blood
Phosphorylation
Rats
Rats, Wistar
Signal Transduction/*physiology
Superoxide Dismutase/metabolism

@article {pmid31221587,
year = {2019},
author = {Aho, VTE and Pereira, PAB and Voutilainen, S and Paulin, L and Pekkonen, E and Auvinen, P and Scheperjans, F},
title = {Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression.},
journal = {EBioMedicine},
volume = {44},
number = {},
pages = {691-707},
doi = {10.1016/j.ebiom.2019.05.064},
pmid = {31221587},
issn = {2352-3964},
mesh = {Aged ; Biodiversity ; Case-Control Studies ; Disease Progression ; *Disease Susceptibility ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics/methods ; Middle Aged ; Parkinson Disease/*etiology/*metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Several publications have described differences in cross-sectional comparisons of gut microbiota between patients with Parkinson's disease and control subjects, with considerable variability of the reported differentially abundant taxa. The temporal stability of such microbiota alterations and their relationship to disease progression have not been previously studied with a high-throughput sequencing based approach.

METHODS: We collected clinical data and stool samples from 64 Parkinson's patients and 64 control subjects twice, on average 2·25 years apart. Disease progression was evaluated based on changes in Unified Parkinson's Disease Rating Scale and Levodopa Equivalent Dose, and microbiota were characterized with 16S rRNA gene amplicon sequencing.

FINDINGS: We compared patients to controls, and patients with stable disease to those with faster progression. There were significant differences between microbial communities of patients and controls when corrected for confounders, but not between timepoints. Specific bacterial taxa that differed between patients and controls at both timepoints included several previously reported ones, such as Roseburia, Prevotella and Bifidobacterium. In progression comparisons, differentially abundant taxa were inconsistent across methods and timepoints, but there was some support for a different distribution of enterotypes and a decreased abundance of Prevotella in faster-progressing patients.

INTERPRETATION: The previously detected gut microbiota differences between Parkinson's patients and controls persisted after 2 years. While we found some evidence for a connection between microbiota and disease progression, a longer follow-up period is required to confirm these findings.},
}

Aged
Biodiversity
Case-Control Studies
Disease Progression
*Disease Susceptibility
Female
*Gastrointestinal Microbiome
High-Throughput Nucleotide Sequencing
Humans
Male
Metagenomics/methods
Middle Aged
Parkinson Disease/*etiology/*metabolism/pathology
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA