@article {pmid31844663,
year = {2019},
author = {Olm, MR and Bhattacharya, N and Crits-Christoph, A and Firek, BA and Baker, R and Song, YS and Morowitz, MJ and Banfield, JF},
title = {Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria.},
journal = {Science advances},
volume = {5},
number = {12},
pages = {eaax5727},
pmid = {31844663},
issn = {2375-2548},
support = {R01 AI092531/AI/NIAID NIH HHS/United States ; R01 GM109454/GM/NIGMS NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; },
mesh = {Enterobacteriaceae/genetics ; Enterocolitis, Necrotizing/*genetics/microbiology ; Feces/microbiology ; Fimbriae, Bacterial/*genetics/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/genetics/microbiology ; Klebsiella/genetics ; *Metagenomics ; Multigene Family/genetics ; },
abstract = {Necrotizing enterocolitis (NEC) is a devastating intestinal disease that occurs primarily in premature infants. We performed genome-resolved metagenomic analysis of 1163 fecal samples from premature infants to identify microbial features predictive of NEC. Features considered include genes, bacterial strain types, eukaryotes, bacteriophages, plasmids, and growth rates. A machine learning classifier found that samples collected before NEC diagnosis harbored significantly more Klebsiella, bacteria encoding fimbriae, and bacteria encoding secondary metabolite gene clusters related to quorum sensing and bacteriocin production. Notably, replication rates of all bacteria, especially Enterobacteriaceae, were significantly higher 2 days before NEC diagnosis. The findings uncover biomarkers that could lead to early detection of NEC and targets for microbiome-based therapeutics.},
}

Enterobacteriaceae/genetics
Enterocolitis, Necrotizing/*genetics/microbiology
Feces/microbiology
Fimbriae, Bacterial/*genetics/microbiology
Gastrointestinal Microbiome/*genetics
Humans
Infant, Newborn
Infant, Premature
Infant, Premature, Diseases/genetics/microbiology
Klebsiella/genetics
*Metagenomics
Multigene Family/genetics

@article {pmid31053581,
year = {2019},
author = {Mandhania, MH and Paul, D and Suryavanshi, MV and Sharma, L and Chowdhury, S and Diwanay, SS and Diwanay, SS and Shouche, YS and Patole, MS},
title = {Diversity and Succession of Microbiota during Fermentation of the Traditional Indian Food Idli.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {13},
pages = {},
pmid = {31053581},
issn = {1098-5336},
mesh = {Bacteria/classification/*isolation & purification ; Breakfast ; *Fermentation ; *Food Microbiology ; India ; *Microbiota ; Oryza/metabolism/*microbiology ; },
abstract = {Idli, a naturally fermented Indian food, is prepared from a mixture of rice and black gram (lentil). To understand its microbial community during fermentation, detailed analysis of the structural and functional dynamics of the idli microbiome was performed by culture-dependent and -independent approaches. The bacterial diversity and microbial succession were assessed at different times of fermentation by 16S rRNA amplicon sequencing. Results highlighted that most microbiota belonged to phylum Firmicutes (70%) and Proteobacteria (22%). Denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) analysis confirmed the diversity and succession involved therein. A culture-dependent approach revealed that the microbially diverse populations were conserved across different geographical locations. The fermentation was primarily driven by lactic acid bacteria as they constitute 86% of the total bacterial population, and genus Weissella emerged as the most important organism in fermentation. The natural microbiota of the grains mainly drives the fermentation, as surface sterilized grains did not show any fermentation. Growth kinetics of idli microbiota and physicochemical parameters corroborated the changes in microbial dynamics, acid production, and leavening occurring during fermentation. Using a metagenomic prediction tool, we found that the major metabolic activities of these microbial fermenters were augmented during the important phase of fermentation. The involvement of the heterofermentative hexose monophosphate (HMP) pathway in batter leavening was substantiated by radiolabeled carbon dioxide generated from d-[1-14C]-glucose. Hydrolases degrading starch and phytins and the production of B vitamins were reported. Moreover, culturable isolates showing beneficial attributes, such as acid and bile tolerance, hydrophobicity, antibiotic sensitivity, and antimicrobial activity, suggest idli to be a potential dietary supplement.IMPORTANCE This is a comprehensive analysis of idli fermentation employing modern molecular tools which provided valuable information about the bacterial diversity enabling its fermentation. The study has demonstrated the relationship between the bacterial population and its functional role in the process. The nature of idli fermentation was found to be more complex than other food fermentations due to the succession of the bacterial population. Further studies using metatranscriptomics and metabolomics may enhance the understanding of this complex fermentation process. Moreover, the presence of microorganisms with beneficial properties plausibly makes idli a suitable functional food.},
}

Bacteria/classification/*isolation & purification
Breakfast
*Fermentation
*Food Microbiology
India
*Microbiota
Oryza/metabolism/*microbiology

@article {pmid32486022,
year = {2020},
author = {Koike, Y and Kuwatsuka, S and Nishimoto, K and Motooka, D and Murota, H},
title = {Skin Mycobiome of Psoriasis Patients is Retained during Treatment with TNF and IL-17 Inhibitors.},
journal = {International journal of molecular sciences},
volume = {21},
number = {11},
pages = {},
doi = {10.3390/ijms21113892},
pmid = {32486022},
issn = {1422-0067},
support = {KHKS20190401015//Kyowa Hakko Kirin/ ; },
abstract = {BACKGROUND: Biological treatment relieves refractory skin lesions in patients with psoriasis; however, changes in the fungal microbiome (the mycobiome) on the skin are unclear.

METHODS: The skin mycobiome of psoriasis patients treated with TNF inhibitors (TNFi, n = 5) and IL-17 inhibitors (IL-17i, n = 7) was compared with that of patients not receiving systemic therapy (n = 7). Skin swab samples were collected from non-lesional post-auricular areas. Fungal DNA was sequenced by ITS1 metagenomic analysis and taxonomic classification was performed.

RESULTS: An average of 37543 reads/sample were analyzed and fungi belonging to 31 genera were detected. The genus Malassezia accounted for >90% of reads in 7/7 samples from the no-therapy group, 4/5 from the TNFi group, and 5/7 from the IL-17i group. Biodiversity was low in those three groups. Few members of the genus trichophyton were detected; the genus Candida was not detected at all. Among the Malassezia species, M. restricta was the major species in 6/7 samples from the no-therapy group, 4/5 from the TNFi group, and 5/7 from the IL-17i group whose the other largest species revealed M. globosa.

CONCLUSIONS: The mycobiome is retained on post-auricular skin during systemic treatment with TNF and IL-17 inhibitors.},
}

@article {pmid31828407,
year = {2020},
author = {Paddock, MB and Fernández-Bayo, JD and VanderGheynst, JS},
title = {The effect of the microalgae-bacteria microbiome on wastewater treatment and biomass production.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {2},
pages = {893-905},
doi = {10.1007/s00253-019-10246-x},
pmid = {31828407},
issn = {1432-0614},
support = {1438211//National Science Foundation/ ; ARV-15-008//California Energy Commission/ ; },
mesh = {Ammonium Compounds/analysis ; Bacteria/classification/*growth & development/*metabolism ; Biological Oxygen Demand Analysis ; Bioreactors/microbiology ; Metagenomics ; Microalgae/classification/*growth & development/*metabolism ; *Microbiota ; Nitrogen/analysis ; Waste Water/chemistry/*microbiology ; Water Pollutants/metabolism ; Water Purification/*methods ; },
abstract = {The use of microalgae for wastewater treatment has been proposed as a cost-effective method to produce biofuels while remediating waste streams. This study examined the microalgae biomass production rate, wastewater treatment efficiency, and prokaryotic organism microbiome associated with microalgae Chlorella sorokiniana cultivated on anaerobic digestate effluent. Final microalgae biomass concentrations from nine photobioreactors were highly variable and had values that ranged between 0.14 g/L and 0.90 g/L. Nutrient removal efficiencies for TN (total nitrogen), N-NH4 (ammonium nitrogen), and COD (chemical oxygen demand) ranged from 34% to 67%, 65% to 97%, and-60% to 14%, respectively. Analysis of individual OTUs (operational taxonomic units) from the microbial community revealed that microalgae biomass concentrations were significantly correlated with the relative abundance of OTUs in the genus Pusillimonas. Predictive metagenomic analyses identified additional correlations associated with biomass production and nutrient removal. These results suggest that the microbial community present during microalgae cultivation on wastewater can impact the performance of the system for biomass production and wastewater treatment.},
}

Ammonium Compounds/analysis
Bacteria/classification/*growth & development/*metabolism
Biological Oxygen Demand Analysis
Bioreactors/microbiology
Metagenomics
Microalgae/classification/*growth & development/*metabolism
*Microbiota
Nitrogen/analysis
Waste Water/chemistry/*microbiology
Water Pollutants/metabolism
Water Purification/*methods

@article {pmid31820070,
year = {2020},
author = {Tyx, RE and Rivera, AJ and Keong, LM and Stanfill, SB},
title = {An exploration of smokeless tobacco product nucleic acids: a combined metagenome and metatranscriptome analysis.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {2},
pages = {751-763},
doi = {10.1007/s00253-019-10232-3},
pmid = {31820070},
issn = {1432-0614},
support = {CC999999/ImCDC/Intramural CDC HHS/United States ; },
mesh = {Bacteria/metabolism ; Biotransformation ; DNA, Bacterial/genetics ; *Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; *Microbiota ; Nitrates/metabolism ; Nitrites/metabolism ; RNA, Bacterial/analysis/genetics ; RNA, Viral/analysis/genetics ; Tobacco, Smokeless/*microbiology ; },
abstract = {Smokeless tobacco (ST) products are used worldwide and are a major public health concern. In addition to harmful chemicals found in these products, microbes found in ST products are believed to be responsible for generating harmful tobacco-specific nitrosamines (TSNAs), the most abundant carcinogens in ST. These microbes also contribute endotoxins and other pro-inflammatory components. A greater understanding of the microbial constituents in these products is sought in order to potentially link select design aspects or manufacturing processes to avoidable increases in harmful constituents. Previous studies looked primarily at bacterial constituents and had not differentiated between viable vs nonviable organisms, so in this study, we sought to use a dual metatranscriptomic and metagenomic analysis to see if differences exist. Using high-throughput sequencing, we observed that there were differences in taxonomic abundances between the metagenome and metatranscriptome, and in the metatranscriptome, we also observed an abundance of plant virus RNA not previously reported in DNA-only studies. We also found in the product tested, that there were no viable bacteria capable of metabolizing nitrate to nitrite. Therefore, the product tested would not be likely to increase TSNAs during shelf storage. We tested only a single product to date using the strategy presented here, but succeeded in demonstrating the value of using of these methods in tobacco products. These results present novel findings from the first combined metagenome and metatranscriptome of a commercial tobacco product.},
}

Bacteria/metabolism
Biotransformation
DNA, Bacterial/genetics
*Gene Expression Profiling
High-Throughput Nucleotide Sequencing
*Metagenomics
*Microbiota
Nitrates/metabolism
Nitrites/metabolism
RNA, Bacterial/analysis/genetics
RNA, Viral/analysis/genetics
Tobacco, Smokeless/*microbiology

@article {pmid31781816,
year = {2020},
author = {Sun, F and Wang, C and Chen, L and Weng, G and Zheng, Z},
title = {The intestinal bacterial community of healthy and diseased animals and its association with the aquaculture environment.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {2},
pages = {775-783},
doi = {10.1007/s00253-019-10236-z},
pmid = {31781816},
issn = {1432-0614},
support = {2017A020216008//Project of Guangdong Science and Technology Department/ ; 2016I1002//Project of Fujian Science and Technology Department/ ; 2017T3010//Project of Fujian Science and Technology Department/ ; },
mesh = {Animals ; Aquaculture ; Bacteria/*classification/*genetics ; Crustacea/*microbiology ; *Gastrointestinal Microbiome ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Water Microbiology ; },
abstract = {Although increasing levels of attention have been targeted towards aquaculture-associated bacteria, the bacterial community of animal intestines and its relationship with the aquaculture environment need to be further investigated. In this study, we used high-throughput sequencing to analyze the bacterial community of pond water, sediment, and the intestines of diseased and healthy animals. Our data showed that Proteobacteria, Firmicutes, Cyanobacteria, and Bacteroidetes were the dominant taxa of bacteria across all samples and accounted for more than 90% of the total sequence. Difference analysis and Venn diagrams showed that most of the intestinal bacterial OTUs (operational taxonomic units) of diseased and healthy animals were the same as those of sediment and water, indicating that the aquaculture environment was the main source of intestinal bacteria. Compared with healthy animals, a considerable reduction of OTUs was evident in diseased animals. Welch's t test showed that the dominant bacterial taxa in sediment, water, and animal intestine were significantly different (p < 0.05) and each had its own unique dominant microorganisms. In addition, differences between the intestinal bacteria of healthy and diseased animals were represented by potential probiotics and pathogens, such as Bacillus, Vibrio, Oceanobacillus, and Lactococcus. Principal component analysis (PcoA) showed that a similar environment shaped a similar microbial structure. There was a large difference in the spectrum of intestinal bacteria in diseased animals; furthermore, the spectrum of intestinal bacteria in diseased animals was very different from the environment than in healthy animals. This study provides a theoretical basis for a relationship between the intestinal bacteria of healthy and diseased animals and the environment and provides guidance for environmental regulation and disease prevention in aquaculture areas.},
}

Animals
Aquaculture
Bacteria/*classification/*genetics
Crustacea/*microbiology
*Gastrointestinal Microbiome
Geologic Sediments/*microbiology
High-Throughput Nucleotide Sequencing
Metagenomics
*Water Microbiology

@article {pmid31419942,
year = {2019},
author = {Shami, A and Al-Mijalli, S and Pongchaikul, P and Al-Barrag, A and AbduRahim, S},
title = {The prevalence of the culturable human skin aerobic bacteria in Riyadh, Saudi Arabia.},
journal = {BMC microbiology},
volume = {19},
number = {1},
pages = {189},
pmid = {31419942},
issn = {1471-2180},
mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacteria, Aerobic/classification/genetics/growth & development/*isolation & purification ; Child ; Female ; Humans ; Male ; Microbiota ; Middle Aged ; Saudi Arabia ; Skin/*microbiology ; Young Adult ; },
abstract = {BACKGROUND: Human skin is an appropriate environment for the growth of different types of microbes that may inhabit the skin as commensal flora. This study aims at identifying the diversity of skin microbiota in healthy Saudi population. In this study, 80 Saudi subjects of both males and females, from different habitat, and different ages (elderly and young), were recruited to determine the aerobic bacterial flora from their three skin sites; hand, scalp and foot. A single colony obtained from aerobic culture was identified using Biomérieux VITEK® 2 system. For those not being identified by VITEK® 2 system, the identification was conducted using 16 s rRNA sequence.

RESULTS: Thirty-three bacterial species were isolated from males, whilst 24 species were isolated from females. Micrococci are the predominant organisms, followed by Staphylococci, Pantoea species, and lastly Enterococcus faecium. Acinetobacter baumannii, Enterococcus faecalis, and Klebsiella pneumoniae were only found in elder subjects, while Pseudomonas aeruginosa was isolated from the young only. The number of bacterial isolates in the elders was higher that of the young. The average number of flora was larger in foot, then hand and lastly scalp.

CONCLUSION: Here we show the difference in the number of cultivable bacteria across age and gender that may result in the variety of local skin infection. This study paves the way to further investigation in the aspect of in-depth metagenomics analysis and host-pathogen interaction.},
}

Adolescent
Adult
Aged
Aged, 80 and over
Bacteria, Aerobic/classification/genetics/growth & development/*isolation & purification
Child
Female
Humans
Male
Microbiota
Middle Aged
Saudi Arabia
Skin/*microbiology
Young Adult

@article {pmid32482859,
year = {2020},
author = {Roach, TNF and Little, M and Arts, MGI and Huckeba, J and Haas, AF and George, EE and Quinn, RA and Cobián-Güemes, AG and Naliboff, DS and Silveira, CB and Vermeij, MJA and Kelly, LW and Dorrestein, PC and Rohwer, F},
title = {A multiomic analysis of in situ coral-turf algal interactions.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1915455117},
pmid = {32482859},
issn = {1091-6490},
abstract = {Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral-turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.},
}

@article {pmid32482169,
year = {2020},
author = {Zhong, H and Lehtovirta-Morley, L and Liu, J and Zheng, Y and Lin, H and Song, D and Todd, JD and Tian, J and Zhang, XH},
title = {Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {78},
doi = {10.1186/s40168-020-00849-2},
pmid = {32482169},
issn = {2049-2618},
support = {91751202//National Natural Science Foundation of China/ ; 41730530//National Natural Science Foundation of China/ ; 41476112//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans-the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the "shallower" deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water.

RESULTS: In this study, metagenomic data were obtained from 0-10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1000-4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea.

CONCLUSIONS: Our study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-sea Thaumarchaeota in carbon and nitrogen cycling. Video Abstract.},
}

@article {pmid31189707,
year = {2019},
author = {Altan, E and Dib, JC and Gulloso, AR and Escribano Juandigua, D and Deng, X and Bruhn, R and Hildebrand, K and Freiden, P and Yamamoto, J and Schultz-Cherry, S and Delwart, E},
title = {Effect of Geographic Isolation on the Nasal Virome of Indigenous Children.},
journal = {Journal of virology},
volume = {93},
number = {17},
pages = {},
pmid = {31189707},
issn = {1098-5514},
support = {HHSN272201400006C/AI/NIAID NIH HHS/United States ; },
mesh = {Biodiversity ; Child ; Child, Preschool ; Colombia ; Female ; Humans ; Indigenous Peoples ; Male ; Metagenomics/*methods ; Nose/*virology ; Phylogeny ; Phylogeography ; Viruses/*classification/isolation & purification ; },
abstract = {The influence of living in small remote villages on the diversity of viruses in the nasal mucosa was investigated in three Colombian villages with very different levels of geographic isolation. Metagenomic analysis was used to characterize viral nucleic acids in nasal swabs from 63 apparently healthy young children. Sequences from human virus members of the families Anelloviridae, Papillomaviridae, Picornaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, and Paramyxoviridae were detected in decreasing proportions of children. The number of papillomavirus infections detected was greater among Hispanic children most exposed to outside contacts, while anellovirus infections were more common in the isolated indigenous villages. The diversity of the other human viruses detected did not differ among the villages. Closely related variants of rhinovirus A or B were identified in 2 to 4 children from each village, reflecting ongoing transmission clusters. Genomes of viruses not currently known to infect humans, including members of the families Parvoviridae, Partitiviridae, Dicistroviridae, and Iflaviridae and circular Rep-encoding single-stranded DNA (CRESS-DNA) virus, were also detected in nasal swabs, possibly reflecting environmental contamination from insect, fungal, or unknown sources. Despite the high levels of geographic and cultural isolation, the overall diversity of human viruses in the nasal passages of children was not reduced in highly isolated indigenous villages, indicating ongoing exposure to globally circulating viruses.IMPORTANCE Extreme geographic and cultural isolation can still be found in some indigenous South American villages. Such isolation may be expected to limit the introduction of otherwise common and widely distributed viruses. Very small population sizes may also result in rapid local viral extinction due to a lack of seronegative subjects to maintain transmission chains for rapidly cleared viruses. We compared the viruses in the nasal passages of young children in three villages with increasing levels of geographic isolation. We found that isolation did not reduce the overall diversity of viral infections. Multiple infections with nearly identical rhinoviruses could be detected within each village, likely reflecting recent viral introductions and transmission clusters among epidemiologically linked members of these very small communities. We conclude that, despite their geographic isolation, remote indigenous villages show evidence of ongoing exposure to globally circulating viruses.},
}

Biodiversity
Child
Child, Preschool
Colombia
Female
Humans
Indigenous Peoples
Male
Metagenomics/*methods
Nose/*virology
Phylogeny
Phylogeography
Viruses/*classification/isolation & purification

@article {pmid31957879,
year = {2020},
author = {Arıkan, M and Mitchell, AL and Finn, RD and Gürel, F},
title = {Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics.},
journal = {Journal of food science},
volume = {85},
number = {2},
pages = {455-464},
pmid = {31957879},
issn = {1750-3841},
support = {215Z672//Türkiye Bilimsel ve Teknolojik Araştirma Kurumu/ ; 20138//Bilimsel Araştirma Projeleri Birimi, Istanbul Üniversitesi/ ; BB/M011755/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R015228/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //European Molecular Biology Laboratory/ ; },
mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; Beverages/*microbiology ; Fermentation ; Fermented Foods and Beverages/*microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; Yeasts/classification/genetics/*isolation & purification/metabolism ; },
abstract = {Kombucha, a fermented tea generated from the co-culture of yeasts and bacteria, has gained worldwide popularity in recent years due to its potential benefits to human health. As a result, many studies have attempted to characterize both its biochemical properties and microbial composition. Here, we have applied a combination of whole metagenome sequencing (WMS) and amplicon (16S rRNA and Internal Transcribed Spacer 1 [ITS1]) sequencing to investigate the microbial communities of homemade Kombucha fermentations from day 3 to day 15. We identified the dominant bacterial genus as Komagataeibacter and dominant fungal genus as Zygosaccharomyces in all samples at all time points. Furthermore, we recovered three near complete Komagataeibacter genomes and one Zygosaccharomyces bailii genome and then predicted their functional properties. Also, we determined the broad taxonomic and functional profile of plasmids found within the Kombucha microbial communities. Overall, this study provides a detailed description of the taxonomic and functional systems of the Kombucha microbial community. Based on this, we conject that the functional complementarity enables metabolic cross talks between Komagataeibacter species and Z. bailii, which helps establish the sustained a relatively low diversity ecosystem in Kombucha.},
}

Bacteria/classification/genetics/*isolation & purification/metabolism
Beverages/*microbiology
Fermentation
Fermented Foods and Beverages/*microbiology
Metagenome
Metagenomics
*Microbiota
Sequence Analysis, DNA
Yeasts/classification/genetics/*isolation & purification/metabolism

@article {pmid31852462,
year = {2019},
author = {Zhang, X and Browman, G and Siu, W and Basen-Engquist, KM and Hanash, SM and Hoffman, KL and Okhuysen, PC and Scheet, P and Petrosino, JF and Kopetz, S and Daniel, CR},
title = {The BE GONE trial study protocol: a randomized crossover dietary intervention of dry beans targeting the gut microbiome of overweight and obese patients with a history of colorectal polyps or cancer.},
journal = {BMC cancer},
volume = {19},
number = {1},
pages = {1233},
pmid = {31852462},
issn = {1471-2407},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; Institutional Research Grant//University of Texas MD Anderson Cancer Center/ ; 5P30 CA016672-37/CA/NCI NIH HHS/United States ; RSG-17-049-01-NEC//American Cancer Society/ ; RP160097//Cancer Prevention and Research Institute of Texas/ ; },
mesh = {Adult ; Aged ; Aged, 80 and over ; Colonic Neoplasms/*diet therapy/microbiology/pathology/prevention & control ; Colonic Polyps/*diet therapy/microbiology/pathology/prevention & control ; Cross-Over Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Life Style ; Male ; Middle Aged ; Obesity/microbiology/*physiopathology ; Overweight/microbiology/*physiopathology ; Progression-Free Survival ; Risk Factors ; },
abstract = {BACKGROUND: Mouse and human studies support the promise of dry beans to improve metabolic health and to lower cancer risk. In overweight/obese patients with a history of colorectal polyps or cancer, the Beans to Enrich the Gut microbiome vs. Obesity's Negative Effects (BE GONE) trial will test whether and how an increase in the consumption of pre-cooked, canned dry beans within the context of usual diet and lifestyle can enhance the gut landscape to improve metabolic health and reduce cancer risk.

METHODS/DESIGN: This randomized crossover trial is designed to characterize changes in (1) host markers spanning lipid metabolism, inflammation, and obesity-related cancer risk; (2) compositional and functional profiles of the fecal microbiome; and (3) host and microbial metabolites. With each subject serving as their own control, the trial will compare the participant's usual diet with (intervention) and without (control) dry beans. Canned, pre-cooked dry beans are provided to participants and the usual diet continually assessed and monitored. Following a 4-week run-in and equilibration period, each participant provides a total of 5 fasting blood and 6 stool samples over a total period of 16 weeks. The intervention consists of a 2-week ramp-up of dry bean intake to 1 cup/d, which is then continued for an additional 6 weeks. Intra- and inter-individual outcomes are assessed across each crossover period with consideration of the joint or modifying effects of the usual diet and baseline microbiome.

DISCUSSION: The BE GONE trial is evaluating a scalable dietary prevention strategy targeting the gut microbiome of high-risk patients to mitigate the metabolic and inflammatory effects of adiposity that influence colorectal cancer risk, recurrence, and survival. The overarching scientific goal is to further elucidate interactions between diet, the gut microbiome, and host metabolism. Improved understanding of the diet-microbiota interplay and effective means to target these relationships will be key to the future of clinical and public health approaches to cancer and other major diet- and obesity-related diseases.

TRIAL REGISTRATION: This protocol is registered with the U.S. National Institutes of Health trial registry, ClinicalTrials.gov, under the identifier NCT02843425. First posted July 25, 2016; last verified January 25, 2019.},
}

Adult
Aged
Aged, 80 and over
Colonic Neoplasms/*diet therapy/microbiology/pathology/prevention & control
Colonic Polyps/*diet therapy/microbiology/pathology/prevention & control
Cross-Over Studies
Female
*Gastrointestinal Microbiome
Humans
Life Style
Male
Middle Aged
Obesity/microbiology/*physiopathology
Overweight/microbiology/*physiopathology
Progression-Free Survival
Risk Factors

@article {pmid31617268,
year = {2020},
author = {Saborío-Montero, A and Gutiérrez-Rivas, M and García-Rodríguez, A and Atxaerandio, R and Goiri, I and López de Maturana, E and Jiménez-Montero, JA and Alenda, R and González-Recio, O},
title = {Structural equation models to disentangle the biological relationship between microbiota and complex traits: Methane production in dairy cattle as a case of study.},
journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie},
volume = {137},
number = {1},
pages = {36-48},
doi = {10.1111/jbg.12444},
pmid = {31617268},
issn = {1439-0388},
support = {RTA2015-00022-CO3 (METALGEN) national plan of rese//national plan of research, development and innovation 2013-2020/ ; RTA2015-00022-CO3//National Plan of Research, Development and Innovation 2013-2020/ ; },
mesh = {Animals ; Cattle/*metabolism/*microbiology ; *Dairying ; Markov Chains ; Methane/*biosynthesis ; *Microbiota ; *Models, Statistical ; Monte Carlo Method ; },
abstract = {The advent of metagenomics in animal breeding poses the challenge of statistically modelling the relationship between the microbiome, the host genetics and relevant complex traits. A set of structural equation models (SEMs) of a recursive type within a Markov chain Monte Carlo (MCMC) framework was proposed here to jointly analyse the host-metagenome-phenotype relationship. A non-recursive bivariate model was set as benchmark to compare the recursive model. The relative abundance of rumen microbes (RA), methane concentration (CH4) and the host genetics was used as a case of study. Data were from 337 Holstein cows from 12 herds in the north and north-west of Spain. Microbial composition from each cow was obtained from whole metagenome sequencing of ruminal content samples using a MinION device from Oxford Nanopore Technologies. Methane concentration was measured with Guardian® NG infrared gas monitor from Edinburgh Sensors during cow's visits to the milking automated system. A quarterly average from the methane eructation peaks for each cow was computed and used as phenotype for CH4 . Heritability of CH4 was estimated at 0.12 ± 0.01 in both the recursive and bivariate models. Likewise, heritability estimates for the relative abundance of the taxa overlapped between models and ranged between 0.08 and 0.48. Genetic correlations between the microbial composition and CH4 ranged from -0.76 to 0.65 in the non-recursive bivariate model and from -0.68 to 0.69 in the recursive model. Regardless of the statistical model used, positive genetic correlations with methane were estimated consistently for the seven genera pertaining to the Ciliophora phylum, as well as for those genera belonging to the Euryarchaeota (Methanobrevibacter sp.), Chytridiomycota (Neocallimastix sp.) and Fibrobacteres (Fibrobacter sp.) phyla. These results suggest that rumen's whole metagenome recursively regulates methane emissions in dairy cows and that both CH4 and the microbiota compositions are partially controlled by the host genotype.},
}

Animals
Cattle/*metabolism/*microbiology
*Dairying
Markov Chains
Methane/*biosynthesis
*Microbiota
*Models, Statistical
Monte Carlo Method

@article {pmid31531910,
year = {2020},
author = {Verschuren, LMG and Schokker, D and Bergsma, R and Jansman, AJM and Molist, F and Calus, MPL},
title = {Prediction of nutrient digestibility in grower-finisher pigs based on faecal microbiota composition.},
journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie},
volume = {137},
number = {1},
pages = {23-35},
pmid = {31531910},
issn = {1439-0388},
support = {BO-22.04-010-001//Breed&Feed4Food/ ; },
mesh = {Animals ; *Digestion ; Feces/*microbiology ; Female ; Male ; *Microbiota ; Nutrients/*metabolism ; Phenotype ; Swine/growth & development/metabolism/*microbiology/*physiology ; },
abstract = {Microbiota play an important role in total tract nutrient digestion, especially when fibrous diets are fed to pigs. This study aimed to use metagenomics to predict faecal nutrient digestibility in grower-finisher pigs. The study design consisted of 160 three-way crossbreed grower-finisher pigs (80 female and 80 male) which were either fed a diet based on corn/soybean meal or a more fibrous diet based on wheat/barley/by-products. On the day before slaughter, faecal samples were collected and used to determine faecal digestibility of dry matter, ash, organic matter, crude protein, crude fat, crude fibre and non-starch polysaccharides. The faecal samples were also sequenced for the 16S hypervariable region of bacteria (V3/V4) to profile the faecal microbiome. With these data, we calculated the between-animal variation in faecal nutrient digestibility associated with variation in the faecal microbiome, that is the "microbiability". The microbiability values were significantly greater than zero for dry matter, organic matter, crude protein, crude fibre and non-starch polysaccharides, ranging from 0.58 to 0.93, as well as for crude fat with a value of 0.37, but not significantly different from zero for ash. Using leave-one-out cross-validation, we estimated the accuracy of predicting digestibility values of individual pigs based on their faecal microbiota composition. The accuracies of prediction for crude fat and ash digestibility were virtually 0, and for the other nutrients, the accuracies ranged from 0.42 to 0.63. In conclusion, the faecal microbiota composition gave high microbiability values for faecal digestibility of dry matter, organic matter, crude protein, crude fibre and non-starch polysaccharides. The accuracies of prediction are relatively low if the interest is in precisely predicting faecal nutrient digestibility of individual pigs, but are promising from the perspective of ranking animals in a genetic selection context.},
}

Animals
*Digestion
Feces/*microbiology
Female
Male
*Microbiota
Nutrients/*metabolism
Phenotype
Swine/growth & development/metabolism/*microbiology/*physiology

@article {pmid31968354,
year = {2020},
author = {Schulz, F and Roux, S and Paez-Espino, D and Jungbluth, S and Walsh, DA and Denef, VJ and McMahon, KD and Konstantinidis, KT and Eloe-Fadrosh, EA and Kyrpides, NC and Woyke, T},
title = {Giant virus diversity and host interactions through global metagenomics.},
journal = {Nature},
volume = {578},
number = {7795},
pages = {432-436},
pmid = {31968354},
issn = {1476-4687},
mesh = {Animals ; *Biodiversity ; Capsid Proteins/genetics ; DNA Viruses/*classification/*genetics ; Eukaryotic Cells/*metabolism/*virology ; Gene Transfer, Horizontal ; Genome, Viral/genetics ; Giant Viruses/classification/genetics ; Host Microbial Interactions/*genetics ; *Metagenomics ; Phylogeny ; },
abstract = {Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes from sampling sites across the globe by building on the rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic diversity and a parallel 10-fold expansion in functional diversity. Analysis of 58,023 major capsid proteins from large and giant viruses using metagenomic data revealed the global distribution patterns and cosmopolitan nature of these viruses. The discovered viral genomes encoded a wide range of proteins with putative roles in photosynthesis and diverse substrate transport processes, indicating that host reprogramming is probably a common strategy in the NCLDVs. Furthermore, inferences of horizontal gene transfer connected viral lineages to diverse eukaryotic hosts. We anticipate that the global diversity of NCLDVs that we describe here will establish giant viruses-which are associated with most major eukaryotic lineages-as important players in ecosystems across Earth's biomes.},
}

Animals
*Biodiversity
Capsid Proteins/genetics
DNA Viruses/*classification/*genetics
Eukaryotic Cells/*metabolism/*virology
Gene Transfer, Horizontal
Genome, Viral/genetics
Giant Viruses/classification/genetics
Host Microbial Interactions/*genetics
*Metagenomics
Phylogeny

@article {pmid31855786,
year = {2020},
author = {Moreno-Mesonero, L and Hortelano, I and Moreno, Y and Ferrús, MA},
title = {Evidence of viable Helicobacter pylori and other bacteria of public health interest associated with free-living amoebae in lettuce samples by next generation sequencing and other molecular techniques.},
journal = {International journal of food microbiology},
volume = {318},
number = {},
pages = {108477},
doi = {10.1016/j.ijfoodmicro.2019.108477},
pmid = {31855786},
issn = {1879-3460},
mesh = {Amoeba/*microbiology ; Bacteria/classification/genetics/isolation & purification ; Food Microbiology ; Food Parasitology ; Helicobacter pylori/genetics/*isolation & purification ; Humans ; Lettuce/*microbiology/*parasitology ; Microbiota/genetics ; Public Health ; Real-Time Polymerase Chain Reaction ; },
abstract = {Vegetables are one of the sources from which Helicobacter pylori can be acquired. This bacterium infects >50% of the global population and is a recognized type I human carcinogen. H. pylori enters into the viable but non-culturable state when it is in the environment, and therefore the use of molecular techniques is much convenient for its detection. Free-living amoebae (FLA) are protozoans found in vegetables. They are transmission vehicles for amoeba-resistant bacteria, among which H. pylori is included. The aim of this study is to study the occurrence and viability of H. pylori from lettuce samples, H. pylori internalized into FLA and the microbiome of FLA isolated from these samples. Special focus was pointed to human pathogenic bacteria. H. pylori was not directly detected in any lettuce sample by means of molecular techniques and neither by culture. However, intra-amoebic H. pylori DNA was detected by means of PMA-qPCR in 55% of the samples and viable intra-amoebic H. pylori cells in 25% of the samples by means of DVC-FISH technique. When FLA microbiome was studied, 21 bacterial genera were part of FLA microbiome in all samples. Helicobacter genus was detected as part of the FLA microbiome in two samples. Other bacteria of public health interest such as Aeromonas sp., Arcobacter sp., Legionella sp., Mycobacterium sp., Pseudomonas sp. and Salmonella sp. were detected as part of FLA microbiome along the analysed samples. This study demonstrates for the first time that H. pylori is internalized as well as alive inside FLA isolated from vegetables. Moreover, this study shows that FLA promote H. pylori detection in environmental samples. In addition, as far as we are aware, this is the first study which studies the microbiome of FLA isolated from vegetables. Among the FLA microbiome, bacteria of public health interest were detected, pointing out that FLA are carriers of these pathogens which can reach humans and cause a public health concern.},
}

Amoeba/*microbiology
Bacteria/classification/genetics/isolation & purification
Food Microbiology
Food Parasitology
Helicobacter pylori/genetics/*isolation & purification
Humans
Lettuce/*microbiology/*parasitology
Microbiota/genetics
Public Health
Real-Time Polymerase Chain Reaction

@article {pmid32307604,
year = {2020},
author = {Jiang, T and Guo, C and Wang, M and Wang, M and You, S and Liu, Y and Zhang, X and Liu, H and Jiang, Y and Shao, H and Liang, Y and McMinn, A},
title = {Isolation and complete genome sequence of a novel cyanophage, S-B05, infecting an estuarine Synechococcus strain: insights into environmental adaptation.},
journal = {Archives of virology},
volume = {165},
number = {6},
pages = {1397-1407},
doi = {10.1007/s00705-020-04595-6},
pmid = {32307604},
issn = {1432-8798},
support = {No. 41906126//Natural Science Foundation of China/ ; No.41976117//Natural Science Foundation of China/ ; No.41676178//Natural Science Foundation of China/ ; LMB20091001//Open research fund of LMB/ ; },
mesh = {Base Composition ; Base Sequence ; China ; *Genome, Viral ; Host Specificity ; Metagenomics ; Myoviridae/*classification/*isolation & purification/ultrastructure ; Open Reading Frames ; Pacific Ocean ; Phylogeny ; Seawater/*virology ; Synechococcus/*virology ; Water Microbiology ; Whole Genome Sequencing ; },
abstract = {A new cyanophage, S-B05, infecting a phycoerythrin-enriched (PE-type) Synechococcus strain was isolated by the liquid infection method, and its morphology and genetic features were examined. Phylogenetic analysis and morphological observation confirmed that S-B05 belongs to the family Myoviridae of the order Caudovirales. Its genome was fully sequenced, and found to be 208,857 bp in length with a G + C content of 39.9%. It contained 280 potential open reading frames and 123 conserved domains. Ninety-eight functional genes responsible for cyanophage structuring and packaging, DNA replication and regulation, and photosynthesis were identified, as well as genes encoding 172 hypothetical proteins. The genome of S-B05 is most similar to that of Prochlorococcus phage P-TIM68. Homologues of open reading frames of S-B05 can be found in various marine environments, as revealed by comparison of the S-B05 genome sequence to sequences in marine viral metagenomic databases. The presence of auxiliary metabolic genes (AMGs) related to photosynthesis, carbon metabolism, and phosphorus assimilation, as well as the phylogenetic relationships based on AMGs and the complete genome sequence, reflect the phage-host interaction mechanism or the specific adaptation strategy of the host to environmental conditions. The genome sequence information reported here will provide an important basis for further study of the adaptive evolution and ecological role of cyanophages and their hosts in the marine environment.},
}

Base Composition
Base Sequence
China
*Genome, Viral
Host Specificity
Metagenomics
Myoviridae/*classification/*isolation & purification/ultrastructure
Open Reading Frames
Pacific Ocean
Phylogeny
Seawater/*virology
Synechococcus/*virology
Water Microbiology
Whole Genome Sequencing

@article {pmid31894129,
year = {2019},
author = {Bhat, AH and Prabhu, P and Balakrishnan, K},
title = {A critical analysis of state-of-the-art metagenomics OTU clustering algorithms.},
journal = {Journal of biosciences},
volume = {44},
number = {6},
pages = {},
pmid = {31894129},
issn = {0973-7138},
mesh = {Algorithms ; Cluster Analysis ; *Computational Biology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*trends ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Software ; },
abstract = {Taxonomic profiling, using hyper-variable regions of 16S rRNA, is one of the important goals in metagenomics analysis. Operational taxonomic unit (OTU) clustering algorithms are the important tools to perform taxonomic profiling by grouping 16S rRNA sequence reads into OTU clusters. Presently various OTU clustering algorithms are available within different pipelines, even some pipelines have implemented more than one clustering algorithms, but there is less literature available for the relative performance and features of these algorithms. This makes the choice of using these methods unclear. In this study five current state-of-the-art OTU clustering algorithms (CDHIT, Mothur's Average Neighbour, SUMACLUST, Swarm, and UCLUST) have been comprehensively evaluated on the metagenomics sequencing data. It was found that in all the datasets, Mothur's average neighbour and Swarm created more number of OTU clusters. Based on normalized mutual information (NMI) and normalized information difference (NID), Swarm and Mothur's average neighbour showed better clustering qualities than others. But in terms of time complexity the greedy algorithms (SUMACLUST, CDHIT, and UCLUST) performed well. So there is a trade-off between quality and time, and it is necessary while analysing large size of 16S rRNA gene sequencing data.},
}

Algorithms
Cluster Analysis
*Computational Biology
High-Throughput Nucleotide Sequencing
Humans
Metagenomics/*trends
Microbiota/*genetics
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
*Software

@article {pmid31284329,
year = {2019},
author = {Aw, W and Fukuda, S},
title = {Protective effects of bifidobacteria against enteropathogens.},
journal = {Microbial biotechnology},
volume = {12},
number = {6},
pages = {1097-1100},
pmid = {31284329},
issn = {1751-7915},
mesh = {Acetates/*metabolism ; Animals ; Anti-Bacterial Agents/*metabolism ; *Antibiosis ; Bifidobacterium/growth & development/*metabolism ; Disease Models, Animal ; Escherichia coli Infections/*prevention & control ; Escherichia coli O157/drug effects/*growth & development ; Gastrointestinal Microbiome ; Metabolome ; Mice ; },
abstract = {Recent major advances in metagenomics and metabolomics technologies have enabled us to collect more data on the gut microbiome and metabolome to evaluate its influence on host health. In this short opinion article, we have chosen to focus on summarizing the protective mechanisms of bifidobacteria, a highly regarded probiotic, and it's metabolite: acetate; against enteropathogens, specifically in the E. coli O157:H7 mice model. We advocate for using a novel approach metabologenomics, which is an integration of metagenomic and metabolomic information on a systems biology-wide approach to better understand this interplay between gut microbiome and host metabolism.},
}

Acetates/*metabolism
Animals
Anti-Bacterial Agents/*metabolism
*Antibiosis
Bifidobacterium/growth & development/*metabolism
Disease Models, Animal
Escherichia coli Infections/*prevention & control
Escherichia coli O157/drug effects/*growth & development
Gastrointestinal Microbiome
Metabolome
Mice

@article {pmid31009573,
year = {2019},
author = {Zhang, X and Figeys, D},
title = {Perspective and Guidelines for Metaproteomics in Microbiome Studies.},
journal = {Journal of proteome research},
volume = {18},
number = {6},
pages = {2370-2380},
doi = {10.1021/acs.jproteome.9b00054},
pmid = {31009573},
issn = {1535-3907},
support = {MOP-114872//CIHR/Canada ; },
mesh = {Computational Biology/methods ; Dysbiosis/genetics/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Proteomics/*methods ; },
abstract = {The microbiome is emerging as a prominent factor affecting human health, and its dysbiosis is associated with various diseases. Compositional profiling of microbiome is increasingly being supplemented with functional characterization. Metaproteomics is intrinsically focused on functional changes and therefore will be an important tool in those studies of the human microbiome. In the past decade, development of new experimental and bioinformatic approaches for metaproteomics has enabled large-scale human metaproteomic studies. However, challenges still exist, and there remains a lack of standardizations and guidelines for properly performing metaproteomic studies on human microbiome. Herein, we provide a perspective of recent developments, the challenges faced, and the future directions of metaproteomics and its applications. In addition, we propose a set of guidelines/recommendations for performing and reporting the results from metaproteomic experiments for the study of human microbiomes. We anticipate that these guidelines will be optimized further as more metaproteomic questions are raised and addressed, and metaproteomic applications are published, so that they are eventually recognized and applied in the field.},
}

Computational Biology/methods
Dysbiosis/genetics/microbiology
Gastrointestinal Microbiome/*genetics
Humans
Metagenome/*genetics
Metagenomics/*methods
Proteomics/*methods

@article {pmid30995692,
year = {2019},
author = {Langer, SG and Gabris, C and Einfalt, D and Wemheuer, B and Kazda, M and Bengelsdorf, FR},
title = {Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters.},
journal = {Microbial biotechnology},
volume = {12},
number = {6},
pages = {1210-1225},
pmid = {30995692},
issn = {1751-7915},
mesh = {Anaerobiosis ; Archaea/classification/genetics/*growth & development ; Bacteria, Anaerobic/classification/genetics/*growth & development ; Biofuels ; Bioreactors/*microbiology ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fungi/classification/genetics/*growth & development ; Manure/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; },
abstract = {Biogas production is a biotechnological process realized by complex bacterial, archaeal and likely fungal communities. Their composition was assessed in nine full-scale biogas plants with distinctly differing feedstock input and process parameters. This study investigated the actually active microbial community members by using a comprehensive sequencing approach based on ribosomal 16S and 28S rRNA fragments. The prevailing taxonomical units of each respective community were subsequently linked to process parameters. Ribosomal rRNA of bacteria, archaea and fungi, respectively, showed different compositions with respect to process parameters and supplied feedstocks: (i) bacterial communities were affected by the key factors temperature and ammonium concentration; (ii) composition of archaea was mainly related to process temperature; and (iii) relative abundance of fungi was linked to feedstocks supplied to the digesters. Anaerobic digesters with a high methane yield showed remarkably similar bacterial communities regarding identified taxonomic families. Although archaeal communities differed strongly on genus level from each other, the respective digesters still showed high methane yields. Functional redundancy of the archaeal communities may explain this effect. 28S rRNA sequences of fungi in all nine full-scale anaerobic digesters were primarily classified as facultative anaerobic Ascomycota and Basidiomycota. Since the presence of ribosomal 28S rRNA indicates that fungi may be active in the biogas digesters, further research should be carried out to examine to which extent they are important players in anaerobic digestion processes.},
}

Anaerobiosis
Archaea/classification/genetics/*growth & development
Bacteria, Anaerobic/classification/genetics/*growth & development
Biofuels
Bioreactors/*microbiology
Cluster Analysis
DNA, Archaeal/chemistry/genetics
DNA, Bacterial/chemistry/genetics
DNA, Fungal/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
Fungi/classification/genetics/*growth & development
Manure/*microbiology
Metagenomics
*Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics
RNA, Ribosomal, 28S/genetics
Sequence Analysis, DNA

@article {pmid30989804,
year = {2019},
author = {Mediavilla, O and Geml, J and Olaizola, J and Oria-de-Rueda, JA and Baldrian, P and Martín-Pinto, P},
title = {Effect of forest fire prevention treatments on bacterial communities associated with productive Boletus edulis sites.},
journal = {Microbial biotechnology},
volume = {12},
number = {6},
pages = {1188-1198},
pmid = {30989804},
issn = {1751-7915},
mesh = {Bacteria/*classification/*genetics ; Basidiomycota/*growth & development ; Cistus/growth & development/*microbiology ; DNA Barcoding, Taxonomic ; Metagenomics ; Microbial Interactions ; *Microbiota ; *Soil Microbiology ; Wildfires/*prevention & control ; },
abstract = {Cistus ladanifer scrublands, traditionally considered as unproductive, have nonetheless been observed to produce large quantities of king bolete (Boletus edulis) fruitbodies. These pyrophytic scrublands are prone to wildfires, which severely affect fungi, hence the need for fire prevention in producing C. ladanifer scrublands. In addition, B. edulis productions have severely decreased in the last years. A deeper understanding of the B. edulis life cycle and of biotic and abiotic factors influencing sporocarp formation is needed to implement management practices that facilitate B. edulis production. For example, some bacteria likely are involved in sporocarp production, representing a key part in the triple symbiosis (plant-fungus-bacteria). In this study, we used soil DNA metabarcoding in C. ladanifer scrublands to (i) assess the effect of site history and fire prevention treatment on bacterial richness and community composition; (ii) test if there was any correlation between various taxonomic groups of bacteria and mycelial biomass and sporocarp production of B. edulis; and to (iii) identify indicator bacteria associated with the most productive B. edulis sites. Our results show that site history drives bacterial richness and community composition, while fire prevention treatments have a weaker, but still detectable effect, particularly in the senescent plots. Sporocarp production correlated positively with genera in Verrucomicrobia. Several genera, e.g. Azospirillum and Gemmatimonas, were identified as indicators of the most productive sites, suggesting a potential biological role in B. edulis fructification. This study provides a better understanding of the triple symbiosis (plant-fungus-bacteria) involved in C. ladanifer-B. edulis systems.},
}

Bacteria/*classification/*genetics
Basidiomycota/*growth & development
Cistus/growth & development/*microbiology
DNA Barcoding, Taxonomic
Metagenomics
Microbial Interactions
*Microbiota
*Soil Microbiology
Wildfires/*prevention & control

@article {pmid30927344,
year = {2019},
author = {Bergsveinson, J and Perry, BJ and Simpson, GL and Yost, CK and Schutzman, RJ and Hall, BD and Cameron, ADS},
title = {Spatial analysis of a hydrocarbon waste-remediating landfarm demonstrates influence of management practices on bacterial and fungal community structure.},
journal = {Microbial biotechnology},
volume = {12},
number = {6},
pages = {1199-1209},
pmid = {30927344},
issn = {1751-7915},
mesh = {Bacteria/*classification/genetics/metabolism ; *Biodegradation, Environmental ; Biotransformation ; Fungi/*classification/genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Hydrocarbons/*metabolism ; Metagenomics ; *Microbiota ; Saskatchewan ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Spatial Analysis ; },
abstract = {Cultivation of dedicated soil plots called 'landfarms' is an effective technology for bioremediation of hydrocarbon waste generated by various industrial practices. To understand the influence of soil conditions on landfarm microbial communities, analysis of bacterial and fungal community structure using next-generation sequencing at different sections and depths was performed across a hydrocarbon-waste landfarm in Regina, Saskatchewan, Canada. While a core set of hydrocarbon-associated bacterial and fungal taxa are present throughout the landfarm, unique bacterial and fungal operational taxonomic units are differentially abundant at sections within the landfarm, which correlate with differences in soil physiochemical properties and management practices. Increased frequency of waste application resulted in strong positive correlations between bacterial community assemblages and elevated amounts of oil, grease and F3 - F4 hydrocarbon fractions. In areas of standing water and lower application of hydrocarbon, microbial community structure correlated with soil pH, trace nutrients and metals. Overall, diversity and structure of bacterial communities remain relatively stable across the landfarm, while in contrast, fungal community structure appears more responsive to soil oxygen conditions. Results are consistent with the hypothesis that years of bioremediation activity have shaped microbial communities; however, several management practices can be undertaken to increase efficiency of remediation, including the removal of standing water and soil tilling across the landfarm.},
}

Bacteria/*classification/genetics/metabolism
*Biodegradation, Environmental
Biotransformation
Fungi/*classification/genetics/metabolism
High-Throughput Nucleotide Sequencing
Hydrocarbons/*metabolism
Metagenomics
*Microbiota
Saskatchewan
Soil/chemistry
*Soil Microbiology
Soil Pollutants/*metabolism
Spatial Analysis

@article {pmid31704882,
year = {2019},
author = {Banskar, S and Detzner, AA and Juarez-Rodriguez, MD and Hozo, I and Gupta, D and Dziarski, R},
title = {The Pglyrp1-Regulated Microbiome Enhances Experimental Allergic Asthma.},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
volume = {203},
number = {12},
pages = {3113-3125},
doi = {10.4049/jimmunol.1900711},
pmid = {31704882},
issn = {1550-6606},
mesh = {Allergens/*immunology ; Animals ; Anti-Bacterial Agents/pharmacology ; Asthma/*etiology/*metabolism/pathology ; Cytokines/*genetics/*metabolism ; Disease Models, Animal ; *Disease Susceptibility ; Immunoglobulin E/immunology ; Immunohistochemistry ; Metagenome ; Metagenomics ; Mice ; Mice, Inbred BALB C ; Mice, Knockout ; *Microbiota/drug effects/immunology ; Pyroglyphidae/immunology ; },
abstract = {Changes in intestinal or respiratory microbiomes in infants correlate with increased incidence of asthma, but the causative role of microbiome in the susceptibility to asthma and the host genes that regulate these changes in microbiome are mostly unknown. In this study, we show that decreased responsiveness to allergic asthma in Pglyrp1-/- mice (lacking bactericidal peptidoglycan recognition protein 1) could be transferred to germ-free wild-type mice by colonization of mothers and newborns with microbiota from Pglyrp1-/- mice. These colonized mice had decreased airway resistance and fewer inflammatory cells, less severe histopathology, and lower levels of IgE and proallergic cytokines and chemokines in the lungs. This microbiome-dependent decreased responsiveness to asthma was most pronounced in colonized germ-free BALB/c mice (genetically predisposed to asthma), only partially evident in outbred germ-free Swiss Webster mice, and marginal in conventional BALB/c mice following depletion of microbiome with antibiotics. Mice with a low asthmatic response colonized with microbiota from Pglyrp1-/- mice had increased abundance of Bacteroidetes and decreased abundance of Firmicutes, Tenericutes, Deferribacteres, and Spirochaetes in the feces and increased abundance of Pasteurella in the oropharynx. These changes in bacterial abundance in the feces and oropharynx correlated with lower asthmatic responses in the lungs. Thus, our results show that Pglyrp1 enhances allergic asthmatic responses primarily through its effect on the host intestinal microbiome and identify several bacteria that may increase or decrease sensitivity to asthma. This effect of microbiome is strong in asthma-prone BALB/c mice and weak in asthma-resistant outbred mice and requires germ-free conditions before colonization with microbiota from Pglyrp1-/- mice.},
}

Allergens/*immunology
Animals
Anti-Bacterial Agents/pharmacology
Asthma/*etiology/*metabolism/pathology
Cytokines/*genetics/*metabolism
Disease Models, Animal
*Disease Susceptibility
Immunoglobulin E/immunology
Immunohistochemistry
Metagenome
Metagenomics
Mice
Mice, Inbred BALB C
Mice, Knockout
*Microbiota/drug effects/immunology
Pyroglyphidae/immunology

@article {pmid31455406,
year = {2019},
author = {Suzuki, Y and Nishijima, S and Furuta, Y and Yoshimura, J and Suda, W and Oshima, K and Hattori, M and Morishita, S},
title = {Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {119},
pmid = {31455406},
issn = {2049-2618},
mesh = {Bacteria/genetics/isolation & purification ; Bacteriophages/*genetics ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Humans ; Interspersed Repetitive Sequences/genetics ; Japan ; Metagenome/*genetics ; Plasmids/*genetics ; },
abstract = {BACKGROUND: Elucidating the ecological and biological identity of extrachromosomal mobile genetic elements (eMGEs), such as plasmids and bacteriophages, in the human gut remains challenging due to their high complexity and diversity.

RESULTS: Here, we show efficient identification of eMGEs as complete circular or linear contigs from PacBio long-read metagenomic data. De novo assembly of PacBio long reads from 12 faecal samples generated 82 eMGE contigs (2.5~666.7-kb), which were classified as 71 plasmids and 11 bacteriophages, including 58 novel plasmids and six bacteriophages, and complete genomes of five diverse crAssphages with terminal direct repeats. In a dataset of 413 gut metagenomes from five countries, many of the identified plasmids were highly abundant and prevalent. The ratio of gut plasmids by our plasmid data is more than twice that in the public database. Plasmids outnumbered bacterial chromosomes three to one on average in this metagenomic dataset. Host prediction suggested that Bacteroidetes-associated plasmids predominated, regardless of microbial abundance. The analysis found several plasmid-enriched functions, such as inorganic ion transport, while antibiotic resistance genes were harboured mostly in low-abundance Proteobacteria-associated plasmids.

CONCLUSIONS: Overall, long-read metagenomics provided an efficient approach for unravelling the complete structure of human gut eMGEs, particularly plasmids.},
}

Bacteria/genetics/isolation & purification
Bacteriophages/*genetics
Feces/*microbiology
*Gastrointestinal Microbiome
Gastrointestinal Tract/*microbiology
Genome, Bacterial
Humans
Interspersed Repetitive Sequences/genetics
Japan
Metagenome/*genetics
Plasmids/*genetics

@article {pmid30420263,
year = {2019},
author = {Lamprecht, P and Fischer, N and Huang, J and Burkhardt, L and Lütgehetmann, M and Arndt, F and Rolfs, I and Kerstein, A and Iking-Konert, C and Laudien, M},
title = {Changes in the composition of the upper respiratory tract microbial community in granulomatosis with polyangiitis.},
journal = {Journal of autoimmunity},
volume = {97},
number = {},
pages = {29-39},
doi = {10.1016/j.jaut.2018.10.005},
pmid = {30420263},
issn = {1095-9157},
mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Arthritis, Rheumatoid/immunology ; Biodiversity ; Case-Control Studies ; Computational Biology/methods ; Disease Susceptibility ; *Dysbiosis ; Female ; Granulomatosis with Polyangiitis/*etiology ; Humans ; Male ; Metagenomics/methods ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S ; Respiratory Mucosa/*microbiology ; Young Adult ; },
abstract = {Dysbiosis¸ i.e. changes in microbial composition at a mucosal interface, is implicated in the pathogenesis of many chronic inflammatory and autoimmune diseases. To assess the composition of the microbial upper respiratory tract (URT) community in patients with granulomatosis with polyangiitis (GPA), we used culture-independent high-throughput methods. In this prospective clinical study, nasal swabs were collected from patients with GPA, patients with rheumatoid arthritis (RA, disease control), and healthy controls. Nasal bacterial taxa were assessed using V3-V4 region 16S rRNA amplicon sequencing. Staphylococcus aureus, Haemophilus influenza, and entero- and rhinoviruses were detected using qPCR. Unbiased metagenomic RNA sequencing (UMERS) was performed in a subset of samples to determine the relative abundance of bacterial, fungal, and viral species. A trend toward reduced microbiome diversity was detected in GPA samples compared with healthy controls. The abundance of bacterial taxa and microbial richness were significantly decreased in GPA samples compared with RA samples. The relative abundance of bacterial families shifted, with increased Planococcaceae and decreased Moraxellaceae, Tissierellaceae, Staphylococcaceae, and Propionibacteriaceae in GPA and RA. Further, decreased abundance of Corynebacteriaceae, and Aerococcaceae was observed in GPA samples. Significantly more colonization of S. aureus was seen in the nasal microbiome of GPA compared with RA and healthy control samples. H. influenzae colonization was also observed in GPA samples. UMERS detected the presence of rhinoviral sequences in some GPA samples. Thus, our study uncovered changes in the URT microbial composition in patients with GPA and RA, suggesting that both immunosuppression and disease background affect the URT microbiome. Complex alterations of host-microbiome interactions in the URT could influence chronic endonasal inflammation in GPA.},
}

Adolescent
Adult
Aged
Aged, 80 and over
Arthritis, Rheumatoid/immunology
Biodiversity
Case-Control Studies
Computational Biology/methods
Disease Susceptibility
*Dysbiosis
Female
Granulomatosis with Polyangiitis/*etiology
Humans
Male
Metagenomics/methods
*Microbiota
Middle Aged
RNA, Ribosomal, 16S
Respiratory Mucosa/*microbiology
Young Adult

@article {pmid30416033,
year = {2019},
author = {van der Meulen, TA and Harmsen, HJM and Vila, AV and Kurilshikov, A and Liefers, SC and Zhernakova, A and Fu, J and Wijmenga, C and Weersma, RK and de Leeuw, K and Bootsma, H and Spijkervet, FKL and Vissink, A and Kroese, FGM},
title = {Shared gut, but distinct oral microbiota composition in primary Sjögren's syndrome and systemic lupus erythematosus.},
journal = {Journal of autoimmunity},
volume = {97},
number = {},
pages = {77-87},
doi = {10.1016/j.jaut.2018.10.009},
pmid = {30416033},
issn = {1095-9157},
mesh = {Adult ; Biodiversity ; Case-Control Studies ; Disease Susceptibility ; Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Lupus Erythematosus, Systemic/diagnosis/*etiology/metabolism ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Mouth Mucosa/*microbiology ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Sjogren's Syndrome/diagnosis/*etiology/metabolism ; },
abstract = {OBJECTIVE: Alterations in the microbiota composition of the gastro-intestinal tract are suspected to be involved in the etiopathogenesis of two closely related systemic inflammatory autoimmune diseases: primary Sjögren's syndrome (pSS) and systemic lupus erythematosus (SLE). Our objective was to assess whether alterations in gut and oral microbiota compositions are specific for pSS and SLE.

METHODS: 16S ribosomal RNA gene sequencing was performed on fecal samples from 39 pSS patients, 30 SLE patients and 965 individuals from the general population, as well as on buccal swab and oral washing samples from the same pSS and SLE patients. Alpha-diversity, beta-diversity and relative abundance of individual bacteria were used as outcome measures. Multivariate analyses were performed to test associations between individual bacteria and disease phenotype, taking age, sex, body-mass index, proton-pump inhibitor use and sequencing-depth into account as possible confounding factors.

RESULTS: Fecal microbiota composition from pSS and SLE patients differed significantly from population controls, but not between pSS and SLE. pSS and SLE patients were characterized by lower bacterial richness, lower Firmicutes/Bacteroidetes ratio and higher relative abundance of Bacteroides species in fecal samples compared with population controls. Oral microbiota composition differed significantly between pSS patients and SLE patients, which could partially be explained by oral dryness in pSS patients.

CONCLUSIONS: pSS and SLE patients share similar alterations in gut microbiota composition, distinguishing patients from individuals in the general population, while oral microbiota composition shows disease-specific differences between pSS and SLE patients.},
}

Adult
Biodiversity
Case-Control Studies
Disease Susceptibility
Dysbiosis
Feces/microbiology
Female
*Gastrointestinal Microbiome
Humans
Lupus Erythematosus, Systemic/diagnosis/*etiology/metabolism
Male
Metagenome
Metagenomics/methods
*Microbiota
Middle Aged
Mouth Mucosa/*microbiology
Phenotype
RNA, Ribosomal, 16S/genetics
Sjogren's Syndrome/diagnosis/*etiology/metabolism

@article {pmid31679421,
year = {2019},
author = {Marques, FZ and Jama, HA and Tsyganov, K and Gill, PA and Rhys-Jones, D and Muralitharan, RR and Muir, J and Holmes, A and Mackay, CR},
title = {Guidelines for Transparency on Gut Microbiome Studies in Essential and Experimental Hypertension.},
journal = {Hypertension (Dallas, Tex. : 1979)},
volume = {74},
number = {6},
pages = {1279-1293},
doi = {10.1161/HYPERTENSIONAHA.119.13079},
pmid = {31679421},
issn = {1524-4563},
mesh = {Animals ; Blood Pressure Determination/methods ; Diet ; Disease Models, Animal ; *Disease Progression ; Essential Hypertension/drug therapy/epidemiology/*physiopathology ; Evidence-Based Medicine ; Female ; Gastrointestinal Microbiome/*genetics/immunology ; Humans ; Incidence ; Male ; Metagenomics ; Mice ; *Practice Guidelines as Topic ; Prognosis ; Risk Assessment ; },
abstract = {Hypertension is a complex and modifiable condition in which environmental factors contribute to both onset and progression. Recent evidence has accumulated for roles of diet and the gut microbiome as environmental factors in blood pressure regulation. However, this is complex because gut microbiomes are a unique feature of each individual reflecting that individual's developmental and environmental history creating caveats for both experimental models and human studies. Here, we describe guidelines for conducting gut microbiome studies in experimental and clinical hypertension. We provide a complete guide for authors on proper design, analyses, and reporting of gut microbiota/microbiome and metabolite studies and checklists that can be used by reviewers and editors to support robust reporting and interpretation. We discuss factors that modulate the gut microbiota in animal (eg, cohort, controls, diet, developmental age, housing, sex, and models used) and human studies (eg, blood pressure measurement and medication, body mass index, demographic characteristics including age, cultural identification, living structure, sex and socioeconomic environment, and exclusion criteria). We also provide best practice advice on sampling, storage of fecal/cecal samples, DNA extraction, sequencing methods (including metagenomics and 16S rRNA), and computational analyses. Finally, we discuss the measurement of short-chain fatty acids, metabolites produced by the gut microbiota, and interpretation of data. These guidelines should support better transparency, reproducibility, and translation of findings in the field of gut microbiota/microbiome in hypertension and cardiovascular disease.},
}

Animals
Blood Pressure Determination/methods
Diet
Disease Models, Animal
*Disease Progression
Essential Hypertension/drug therapy/epidemiology/*physiopathology
Evidence-Based Medicine
Female
Gastrointestinal Microbiome/*genetics/immunology
Humans
Incidence
Male
Metagenomics
Mice
*Practice Guidelines as Topic
Prognosis
Risk Assessment

@article {pmid31526447,
year = {2019},
author = {Ravi, A and Halstead, FD and Bamford, A and Casey, A and Thomson, NM and van Schaik, W and Snelson, C and Goulden, R and Foster-Nyarko, E and Savva, GM and Whitehouse, T and Pallen, MJ and Oppenheim, BA},
title = {Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients.},
journal = {Microbial genomics},
volume = {5},
number = {9},
pages = {},
pmid = {31526447},
issn = {2057-5858},
support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BBS/E/F/00044414/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Biodiversity ; Critical Illness ; Enterococcus faecium/isolation & purification/physiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/drug effects ; Humans ; Intensive Care Units ; Male ; Meropenem/pharmacology/therapeutic use ; Metagenomics ; Middle Aged ; Prospective Studies ; },
abstract = {Among long-stay critically ill patients in the adult intensive care unit (ICU), there are often marked changes in the complexity of the gut microbiota. However, it remains unclear whether such patients might benefit from enhanced surveillance or from interventions targeting the gut microbiota or the pathogens therein. We therefore undertook a prospective observational study of 24 ICU patients, in which serial faecal samples were subjected to shotgun metagenomic sequencing, phylogenetic profiling and microbial genome analyses. Two-thirds of the patients experienced a marked drop in gut microbial diversity (to an inverse Simpson's index of <4) at some stage during their stay in the ICU, often accompanied by the absence or loss of potentially beneficial bacteria. Intravenous administration of the broad-spectrum antimicrobial agent meropenem was significantly associated with loss of gut microbial diversity, but the administration of other antibiotics, including piperacillin/tazobactam, failed to trigger statistically detectable changes in microbial diversity. In three-quarters of ICU patients, we documented episodes of gut domination by pathogenic strains, with evidence of cryptic nosocomial transmission of Enterococcus faecium. In some patients, we also saw an increase in the relative abundance of apparent commensal organisms in the gut microbiome, including the archaeal species Methanobrevibacter smithii. In conclusion, we have documented a dramatic absence of microbial diversity and pathogen domination of the gut microbiota in a high proportion of critically ill patients using shotgun metagenomics.},
}

Adult
Aged
Aged, 80 and over
Anti-Bacterial Agents/pharmacology/therapeutic use
*Biodiversity
Critical Illness
Enterococcus faecium/isolation & purification/physiology
Feces/microbiology
Female
*Gastrointestinal Microbiome/drug effects
Humans
Intensive Care Units
Male
Meropenem/pharmacology/therapeutic use
Metagenomics
Middle Aged
Prospective Studies

@article {pmid32109809,
year = {2020},
author = {Zhang, L and Zhang, Y and Patterson, J and Arslan, M and Zhang, Y and Gamal El-Din, M},
title = {Biofiltration of oil sands process water in fixed-bed biofilm reactors shapes microbial community structure for enhanced degradation of naphthenic acids.},
journal = {The Science of the total environment},
volume = {718},
number = {},
pages = {137028},
doi = {10.1016/j.scitotenv.2020.137028},
pmid = {32109809},
issn = {1879-1026},
mesh = {Biodegradation, Environmental ; Biofilms ; Carboxylic Acids ; Filtration ; *Microbiota ; Oil and Gas Fields ; Ozone ; Water Pollutants, Chemical ; },
abstract = {Naphthenic acids (NAs) are a complex mixture of carboxylic acids present in oil sands process water (OSPW). Their recalcitrant nature makes them difficult to be removed from the environment using conventional remediation strategies. This study hypothesized that, upon continuous operation, biofiltration of OSPW in fixed-bed biofilm reactors would allow the development of NA-degrading microbial community within the biofilter following successful removal. Both raw and ozonated OSPW were treated in the biofilters and changes in microbial community were tested via 16S/18S amplicon sequencing and metatranscriptomics. Through switch from suspended growth to attached growth, a shift in indigenous microbial community was seen following by an increase in alpha diversity. Concomitantly, improved degradation of NAs was monitored, i.e., 35.8% and 69.4% of NAs were removed from raw and ozonated OSPW, respectively. Metatranscriptomics analysis suggested the presence of genes involved in the degradation of organic acids and petroleum-related compounds. Specifically, functional abundance of aromatic compounds' metabolism improved from 0.05% to 0.76%; whereas abundance of benzoate transport and degradation pathway increased from 0.04% to 0.64%. These changes conclude that continuous operation of OSPW in the bioreactors was in favor of shaping the overall microbiome towards better NA degradation.},
}

Biodegradation, Environmental
Biofilms
Carboxylic Acids
Filtration
*Microbiota
Oil and Gas Fields
Ozone
Water Pollutants, Chemical

@article {pmid32200249,
year = {2020},
author = {Santos, A and Rachid, C and Pacheco, AB and Magalhães, V},
title = {Biotic and abiotic factors affect microcystin-LR concentrations in water/sediment interface.},
journal = {Microbiological research},
volume = {236},
number = {},
pages = {126452},
doi = {10.1016/j.micres.2020.126452},
pmid = {32200249},
issn = {1618-0623},
mesh = {Biodegradation, Environmental ; Cyanobacteria/*metabolism ; Genes, Bacterial ; Geologic Sediments/analysis/*microbiology ; *Harmful Algal Bloom ; Humans ; Hydrogen-Ion Concentration ; Lakes/microbiology ; Metagenomics ; Microbiota/*genetics ; *Microcystins/analysis ; RNA, Ribosomal, 16S/genetics ; Temperature ; Water/analysis ; Water Pollutants, Chemical/*analysis ; },
abstract = {Harmful cyanobacterial blooms are increasingly common in aquatic environments. This can lead to higher concentrations of cyanotoxins, such as microcystins (MCs), posing a great risk to diverse organisms, including humans. MCs are among the most commonly reported cyanotoxins in freshwater environments worldwide, where they may have different fates. MCs can adsorb to suspended particles into the water column and deposit onto the sediment where they can be affected by physical factors (e.g. winds in shallow lakes causing sediment resuspension) or biological factors (e.g. biodegradation). Here we focused on the conditions of a coastal shallow lagoon contaminated by MCs aiming to estimate the return of pre-existing MCs from the sediment to the water column, to evaluate the adsorption of dissolved MC-LR to the sediment and to verify the occurrence of biodegradation. In experiments with sediment, desorption and adsorption were tested under the influence of temperature, pH and aeration, reproducing conditions observed in the lagoon. MC-desorption was not detected under the tested conditions. Spiking MC-LR into lagoon water samples in the presence of sediment resulted in a 50 % reduction of soluble MC-LR concentration in control conditions (25 °C, pH 8.0, no aeration). Increasing temperature (45 °C) or introducing aeration further stimulated MC-LR removal from the water. Biodegradation was observed in sediment samples and interstitial water (even with tetracycline). The composition of the bacterial community differed in sediment and interstitial water: major phyla were Chloroflexi, Proteobacteria, Firmicutes, and OP3. From the assigned OTUs, we identified genera already described as MC degrading bacteria. Thus, the sediment is a key factor influencing the fate of MC-LR in this shallow coastal lake contributing to stable adsorption and biodegradation.},
}

Biodegradation, Environmental
Cyanobacteria/*metabolism
Genes, Bacterial
Geologic Sediments/analysis/*microbiology
*Harmful Algal Bloom
Humans
Hydrogen-Ion Concentration
Lakes/microbiology
Metagenomics
Microbiota/*genetics
*Microcystins/analysis
RNA, Ribosomal, 16S/genetics
Temperature
Water/analysis
Water Pollutants, Chemical/*analysis

@article {pmid32155560,
year = {2020},
author = {Duan, JL and Sun, JW and Ji, MM and Ma, Y and Cui, ZT and Tian, RK and Xu, PC and Sun, WL and Yuan, XZ},
title = {Indicatory bacteria and chemical composition related to sulfur distribution in the river-lake systems.},
journal = {Microbiological research},
volume = {236},
number = {},
pages = {126453},
doi = {10.1016/j.micres.2020.126453},
pmid = {32155560},
issn = {1618-0623},
mesh = {*Bacteria/classification/genetics ; Biodiversity ; China ; Genes, Bacterial ; Geologic Sediments/chemistry/microbiology ; Lakes/*chemistry/microbiology ; Metagenomics ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S ; Rivers/*chemistry/microbiology ; *Sentinel Species/classification/genetics ; Sulfur/*analysis ; Water Pollutants, Chemical/analysis ; },
abstract = {Sulfate related water quality and trophic status are crucial to operation of water diversion. Though the sulfur geochemistry in the lake sediment have been well studied, the effective indicator of surrounding environment conditions related to sulfur in river-lake systems are still unknown. In this study, Dongping Lake (DPH), Weishan Lake (WSH), and Hanzhuang trunk canal (HZQ) were selected as the typical river-lake systems in the eastern of China. Different spatial variations in sedimentary sulfate, total sulfur, and elemental composition of sediments were investigated in these areas. The relatively high sulfate in surface water and sediments appeared in portions of WSH. The biodiversity of HZQ and WSH surface sediments was much higher than that of DPH. Pseudomonas, Acinetobacter, and Thiobacillus were the dominant genera of the river-lake systems. Among the different genera in distribution, genera such as Malikia, Sulfurovum and Lysinibacillus were significantly negatively correlated with sulfur related environmental factors. While the genera such as Pseudomonas, Vogesella and Acinetobacter were significantly positively correlated with these factors. Compared with connectivity in the largest interaction network, bacteria such as Proteus, Acidobacter and Chlorobacteria were identified as indicatory taxa to infer sulfate related conditions in the river-lake systems.},
}

*Bacteria/classification/genetics
Biodiversity
China
Genes, Bacterial
Geologic Sediments/chemistry/microbiology
Lakes/*chemistry/microbiology
Metagenomics
Microbiota/genetics
Phylogeny
RNA, Ribosomal, 16S
Rivers/*chemistry/microbiology
*Sentinel Species/classification/genetics
Sulfur/*analysis
Water Pollutants, Chemical/analysis

@article {pmid31696235,
year = {2020},
author = {Mitchell, AL and Almeida, A and Beracochea, M and Boland, M and Burgin, J and Cochrane, G and Crusoe, MR and Kale, V and Potter, SC and Richardson, LJ and Sakharova, E and Scheremetjew, M and Korobeynikov, A and Shlemov, A and Kunyavskaya, O and Lapidus, A and Finn, RD},
title = {MGnify: the microbiome analysis resource in 2020.},
journal = {Nucleic acids research},
volume = {48},
number = {D1},
pages = {D570-D578},
pmid = {31696235},
issn = {1362-4962},
support = {BB/M011755/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R015228/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N018354/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; DNA, Ribosomal Spacer/genetics ; Databases, Genetic ; *Metagenome ; Metagenomics/methods ; *Microbiota ; *Phylogeny ; *Software ; },
abstract = {MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. Biochemical pathways and systems predictions have also been added for assembled contigs. MGnify's growing focus on the assembly of metagenomic data has also seen the number of datasets it has assembled and analysed increase six-fold. The non-redundant protein database constructed from the proteins encoded by these assemblies now exceeds 1 billion sequences. Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the assembled contigs and their enriched annotations.},
}

Archaea/classification/genetics
Bacteria/classification/genetics
DNA, Ribosomal Spacer/genetics
Databases, Genetic
*Metagenome
Metagenomics/methods
*Microbiota
*Phylogeny
*Software

@article {pmid31504765,
year = {2020},
author = {Wu, S and Sun, C and Li, Y and Wang, T and Jia, L and Lai, S and Yang, Y and Luo, P and Dai, D and Yang, YQ and Luo, Q and Gao, NL and Ning, K and He, LJ and Zhao, XM and Chen, WH},
title = {GMrepo: a database of curated and consistently annotated human gut metagenomes.},
journal = {Nucleic acids research},
volume = {48},
number = {D1},
pages = {D545-D553},
pmid = {31504765},
issn = {1362-4962},
mesh = {*Databases, Genetic ; *Gastrointestinal Microbiome ; Genes, Bacterial ; Genome, Human ; Humans ; *Metagenome ; Metagenomics/*methods ; Molecular Sequence Annotation ; *Software ; },
abstract = {GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purpose is to facilitate the reusability and accessibility of the rapidly growing human metagenomic data. This is achieved by consistently annotating the microbial contents of collected samples using state-of-art toolsets and by manual curation of the meta-data of the corresponding human hosts. GMrepo organizes the collected samples according to their associated phenotypes and includes all possible related meta-data such as age, sex, country, body-mass-index (BMI) and recent antibiotics usage. To make relevant information easier to access, GMrepo is equipped with a graphical query builder, enabling users to make customized, complex and biologically relevant queries. For example, to find (1) samples from healthy individuals of 18 to 25 years old with BMIs between 18.5 and 24.9, or (2) projects that are related to colorectal neoplasms, with each containing >100 samples and both patients and healthy controls. Precomputed species/genus relative abundances, prevalence within and across phenotypes, and pairwise co-occurrence information are all available at the website and accessible through programmable interfaces. So far, GMrepo contains 58 903 human gut samples/runs (including 17 618 metagenomes and 41 285 amplicons) from 253 projects concerning 92 phenotypes. GMrepo is freely available at: https://gmrepo.humangut.info.},
}

*Databases, Genetic
*Gastrointestinal Microbiome
Genes, Bacterial
Genome, Human
Humans
*Metagenome
Metagenomics/*methods
Molecular Sequence Annotation
*Software

@article {pmid31373710,
year = {2019},
author = {Koopman, N and Molinaro, A and Nieuwdorp, M and Holleboom, AG},
title = {Review article: can bugs be drugs? The potential of probiotics and prebiotics as treatment for non-alcoholic fatty liver disease.},
journal = {Alimentary pharmacology & therapeutics},
volume = {50},
number = {6},
pages = {628-639},
doi = {10.1111/apt.15416},
pmid = {31373710},
issn = {1365-2036},
support = {016.146.327//ZONMW-VIDI/International ; //Dutch Heart Foundation/International ; //Gilead Research scholarship/International ; //Amsterdam UMC Fellowship/International ; //TKI-PPP/International ; },
mesh = {Animals ; Bariatric Surgery ; Fecal Microbiota Transplantation ; Humans ; Microbiota ; Non-alcoholic Fatty Liver Disease/*therapy ; *Prebiotics ; Probiotics/*therapeutic use ; Synbiotics ; },
abstract = {BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) has become the most common chronic liver condition. A major current research effort is ongoing to find potential strategies to treat NAFLD-non-alcoholic steatohepatitis (NASH), with special attention to the gut microbiota. Multiple animal studies and pilot clinical trials are assessing different gut microbiota modulating strategies such as faecal microbiota transplantation, antibiotics, probiotics, prebiotics and synbiotics.

AIM: To review the role of microbiota in NAFLD-NASH and determine whether pro- and prebiotics have potential as treatment METHODS: Information was obtained from critically reviewing literature on PubMed on targeting the gut microbiota in NAFLD. Search terms included NAFLD, NASH, non-alcoholic fatty liver disease, steatohepatitis; combined with microbiome, microbiota, gut bacteria, probiotics and prebiotics.

RESULTS: Animal studies and the first emerging studies in humans show promising results for both the common probiotics Lactobacillus, Bifidobacterium and Streptococci as for short chain fatty acid (SCFA) butyrate-producing bacteria. Also, prebiotics have positive effects on different mechanisms underlying NAFLD-NASH.

CONCLUSIONS: The most promising strategies thus far developed to alter the microbiome in NAFLD-NASH are probiotics and prebiotics. However, pre- and probiotic treatment of NAFLD-NASH is relatively new and still under development. Actual understanding of the involved mechanisms is lacking and changes in the intestinal microbiota composition after treatment are rarely measured. Furthermore, large clinical trials with comparative endpoints are unavailable. Personalised treatment based on metagenomics gut microbiota analysis will probably be part of the future diagnosis and treatment of NAFLD-NASH.},
}

Animals
Bariatric Surgery
Fecal Microbiota Transplantation
Humans
Microbiota
Non-alcoholic Fatty Liver Disease/*therapy
*Prebiotics
Probiotics/*therapeutic use
Synbiotics

@article {pmid31290099,
year = {2019},
author = {Wang, P and Niu, B},
title = {Plant specialized metabolites modulate root microbiomes.},
journal = {Science China. Life sciences},
volume = {62},
number = {8},
pages = {1111-1113},
doi = {10.1007/s11427-019-9579-6},
pmid = {31290099},
issn = {1869-1889},
mesh = {Biosynthetic Pathways ; Gene Expression Regulation, Bacterial ; Metabolomics ; Metagenomics ; Microbiota/*genetics ; Mutation ; Plant Roots/*metabolism ; Plants/*metabolism ; Soil/chemistry ; Soil Microbiology ; Terpenes/metabolism ; Triterpenes/metabolism ; },
}

Biosynthetic Pathways
Gene Expression Regulation, Bacterial
Metabolomics
Metagenomics
Microbiota/*genetics
Mutation
Plant Roots/*metabolism
Plants/*metabolism
Soil/chemistry
Soil Microbiology
Terpenes/metabolism
Triterpenes/metabolism

@article {pmid30952661,
year = {2019},
author = {Yu, J and Deem, LM and Crow, SE and Deenik, J and Penton, CR},
title = {Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential after 2 Years of Biochar Amendment in a Tropical Oxisol.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {11},
pages = {},
pmid = {30952661},
issn = {1098-5336},
mesh = {Agriculture ; Biodiversity ; Carbon ; Carbon Dioxide ; Charcoal/*metabolism/pharmacology ; Denitrification ; Metabolic Networks and Pathways ; *Metagenomics ; Microbiota/drug effects/*physiology ; Nitrous Oxide ; Nutrients/*metabolism ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {The complex structural and functional responses of agricultural soil microbial communities to the addition of carbonaceous compounds such as biochar remain poorly understood. This severely limits the predictive ability for both the potential enhancement of soil fertility and greenhouse gas mitigation. In this study, we utilized shotgun metagenomics in order to decipher changes in the microbial community in soil microcosms after 14 days of incubation at 23°C, which contained soils from biochar-amended and control plots cultivated with Napier grass. Our analyses revealed that biochar-amended soil microbiomes exhibited significant shifts in both community composition and predicted metabolism. Key metabolic pathways related to carbon turnover, such as the utilization of plant-derived carbohydrates as well as denitrification, were enriched under biochar amendment. These community shifts were in part associated with increased soil carbon, such as labile and aromatic carbon compounds, which was likely stimulated by the increased available nutrients associated with biochar amendment. These findings indicate that the soil microbiome response to the combination of biochar addition and to incubation conditions confers enhanced nutrient cycling and a small decrease in CO2 emissions and potentially mitigates nitrous oxide emissions.IMPORTANCE The incorporation of biochar into soil is a promising management strategy for sustainable agriculture owing to its potential to sequester carbon and improve soil fertility. Expanding the addition of biochar to large-scale agriculture hinges on its lasting beneficial effects on the microbial community. However, there exists a significant knowledge gap regarding the specific role that biochar plays in altering the key biological soil processes that influence plant growth and carbon storage in soil. Previous studies that examined the soil microbiome under biochar amendment principally characterized only how the composition alters in response to biochar amendment. In the present study, we shed light on the functional alterations of the microbial community response 2 years after biochar amendment. Our results show that biochar increased the abundance of genes involved in denitrification and carbon turnover and that biochar-amended soil microcosms had a reduction in cumulative CO2 production.},
}

Agriculture
Biodiversity
Carbon
Carbon Dioxide
Charcoal/*metabolism/pharmacology
Denitrification
Metabolic Networks and Pathways
*Metagenomics
Microbiota/drug effects/*physiology
Nitrous Oxide
Nutrients/*metabolism
Phylogeny
Soil/chemistry
*Soil Microbiology

@article {pmid30365027,
year = {2019},
author = {Shi, W and Qi, H and Sun, Q and Fan, G and Liu, S and Wang, J and Zhu, B and Liu, H and Zhao, F and Wang, X and Hu, X and Li, W and Liu, J and Tian, Y and Wu, L and Ma, J},
title = {gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data.},
journal = {Nucleic acids research},
volume = {47},
number = {D1},
pages = {D637-D648},
pmid = {30365027},
issn = {1362-4962},
mesh = {*Databases, Genetic ; *Metagenome ; Metagenomics/*methods/standards ; *Microbiota ; Reference Standards ; *Software ; },
abstract = {Meta-omics approaches have been increasingly used to study the structure and function of the microbial communities. A variety of large-scale collaborative projects are being conducted to encompass samples from diverse environments and habitats. This change has resulted in enormous demands for long-term data maintenance and capacity for data analysis. The Global Catalogue of Metagenomics (gcMeta) is a part of the 'Chinese Academy of Sciences Initiative of Microbiome (CAS-CMI)', which focuses on studying the human and environmental microbiome, establishing depositories of samples, strains and data, as well as promoting international collaboration. To accommodate and rationally organize massive datasets derived from several thousands of human and environmental microbiome samples, gcMeta features a database management system for archiving and publishing data in a standardized way. Another main feature is the integration of more than ninety web-based data analysis tools and workflows through a Docker platform which enables data analysis by using various operating systems. This platform has been rapidly expanding, and now hosts data from the CAS-CMI and a number of other ongoing research projects. In conclusion, this platform presents a powerful and user-friendly service to support worldwide collaborative efforts in the field of meta-omics research. This platform is freely accessible at https://gcmeta.wdcm.org/.},
}

*Databases, Genetic
*Metagenome
Metagenomics/*methods/standards
*Microbiota
Reference Standards
*Software

@article {pmid30252023,
year = {2019},
author = {Plaza Oñate, F and Le Chatelier, E and Almeida, M and Cervino, ACL and Gauthier, F and Magoulès, F and Ehrlich, SD and Pichaud, M},
title = {MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data.},
journal = {Bioinformatics (Oxford, England)},
volume = {35},
number = {9},
pages = {1544-1552},
pmid = {30252023},
issn = {1367-4811},
mesh = {Genome, Bacterial ; Genome, Microbial ; Humans ; Metagenome ; *Metagenomics ; *Microbiota ; Software ; },
abstract = {MOTIVATION: Analysis toolkits for shotgun metagenomic data achieve strain-level characterization of complex microbial communities by capturing intra-species gene content variation. Yet, these tools are hampered by the extent of reference genomes that are far from covering all microbial variability, as many species are still not sequenced or have only few strains available. Binning co-abundant genes obtained from de novo assembly is a powerful reference-free technique to discover and reconstitute gene repertoire of microbial species. While current methods accurately identify species core parts, they miss many accessory genes or split them into small gene groups that remain unassociated to core clusters.

RESULTS: We introduce MSPminer, a computationally efficient software tool that reconstitutes Metagenomic Species Pan-genomes (MSPs) by binning co-abundant genes across metagenomic samples. MSPminer relies on a new robust measure of proportionality coupled with an empirical classifier to group and distinguish not only species core genes but accessory genes also. Applied to a large scale metagenomic dataset, MSPminer successfully delineates in a few hours the gene repertoires of 1661 microbial species with similar specificity and higher sensitivity than existing tools. The taxonomic annotation of MSPs reveals microorganisms hitherto unknown and brings coherence in the nomenclature of the species of the human gut microbiota. The provided MSPs can be readily used for taxonomic profiling and biomarkers discovery in human gut metagenomic samples. In addition, MSPminer can be applied on gene count tables from other ecosystems to perform similar analyses.

The binary is freely available for non-commercial users at www.enterome.com/downloads.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

Genome, Bacterial
Genome, Microbial
Humans
Metagenome
*Metagenomics
*Microbiota
Software

@article {pmid32416615,
year = {2020},
author = {Cordier, T and Alonso-Sáez, L and Apothéloz-Perret-Gentil, L and Aylagas, E and Bohan, DA and Bouchez, A and Chariton, A and Creer, S and Frühe, L and Keck, F and Keeley, N and Laroche, O and Leese, F and Pochon, X and Stoeck, T and Pawlowski, J and Lanzén, A},
title = {Ecosystems monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.15472},
pmid = {32416615},
issn = {1365-294X},
abstract = {A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (A) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (B) De novo bioindicator analyses; (C) Structural community metrics including inferred ecological networks; and (D) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programs that leverage recent analytical advancements, while pointing out current limitations and future research needs.},
}

@article {pmid32414048,
year = {2020},
author = {Kuramae, EE and Derksen, S and Schlemper, TR and Dimitrov, MR and Costa, OYA and Silveira, APDD},
title = {Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics.},
journal = {Microorganisms},
volume = {8},
number = {5},
pages = {},
doi = {10.3390/microorganisms8050725},
pmid = {32414048},
issn = {2076-2607},
support = {729.004.013//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 456420/2013-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Bacteria from the genera Paraburkholderia and Herbaspirillum can promote the growth of Sorghum bicolor, but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized substrate were inoculated with Paraburkholderia tropica strain IAC/BECa 135 and Herbaspirillumfrisingense strain IAC/BECa 152 under phosphate-deficient conditions. These strains significantly increased Sorghum bicolor cultivar SRN-39 root and shoot biomass. Shotgun metagenomic analysis of the rhizosphere revealed successful colonization by both strains; however, the incidence of colonization was higher in plants inoculated with P. tropica strain IAC/BECa 135 than in those inoculated with H. frisingense strain IAC/BECa 152. Conversely, plants inoculated with H. frisingense strain IAC/BECa 152 showed the highest increase in biomass. Genomic analysis of the two inoculants implied a high degree of rhizosphere fitness of P. tropica strain IAC/BECa 135 through environmental signal processing, biofilm formation, and nutrient acquisition. Both genomes contained genes related to plant growth-promoting bacterial (PGPB) traits, including genes related to indole-3-acetate (IAA) synthesis, nitrogen fixation, nodulation, siderophore production, and phosphate solubilization, although the P. tropica strain IAC/BECa 135 genome contained a slightly more extensive repertoire. This study provides evidence that complementary mechanisms of growth promotion in Sorghum might occur, i.e., that P. tropica strain IAC/BECa 135 acts in the rhizosphere and increases the availability of nutrients, while H. frisingense strain IAC/BECa 152 influences plant hormone signaling. While the functional and taxonomic profiles of the rhizobiomes were similar in all treatments, significant differences in plant biomass were observed, indicating that the rhizobiome and the endophytic microbial community may play equally important roles in the complicated plant-microbial interplay underlying increased host plant growth.},
}

@article {pmid32171248,
year = {2020},
author = {Liu, T and Chen, CY and Chen-Deng, A and Chen, YL and Wang, JY and Hou, YI and Lin, MC},
title = {Joining Illumina paired-end reads for classifying phylogenetic marker sequences.},
journal = {BMC bioinformatics},
volume = {21},
number = {1},
pages = {105},
pmid = {32171248},
issn = {1471-2105},
support = {107-2221-E-006-198-MY2//Ministry of Science and Technology, Taiwan/ ; },
mesh = {Asthma/microbiology ; Bacteria/genetics ; Child ; Cluster Analysis ; Genetic Markers ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome ; Metagenomics/methods ; Microbiota/genetics ; *Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: Illumina sequencing of a marker gene is popular in metagenomic studies. However, Illumina paired-end (PE) reads sometimes cannot be merged into single reads for subsequent analysis. When mergeable PE reads are limited, one can simply use only first reads for taxonomy annotation, but that wastes information in the second reads. Presumably, including second reads should improve taxonomy annotation. However, a rigorous investigation of how best to do this and how much can be gained has not been reported.

RESULTS: We evaluated two methods of joining as opposed to merging PE reads into single reads for taxonomy annotation using simulated data with sequencing errors. Our rigorous evaluation involved several top classifiers (RDP classifier, SINTAX, and two alignment-based methods) and realistic benchmark datasets. For most classifiers, read joining ameliorated the impact of sequencing errors and improved the accuracy of taxonomy predictions. For alignment-based top-hit classifiers, rearranging the reference sequences is recommended to avoid improper alignments of joined reads. For word-counting classifiers, joined reads could be compared to the original reference for classification. We also applied read joining to our own real MiSeq PE data of nasal microbiota of asthmatic children. Before joining, trimming low quality bases was necessary for optimizing taxonomy annotation and sequence clustering. We then showed that read joining increased the amount of effective data for taxonomy annotation. Using these joined trimmed reads, we were able to identify two promising bacterial genera that might be associated with asthma exacerbation.

CONCLUSIONS: When mergeable PE reads are limited, joining them into single reads for taxonomy annotation is always recommended. Reference sequences may need to be rearranged accordingly depending on the classifier. Read joining also relaxes the constraint on primer selection, and thus may unleash the full capacity of Illumina PE data for taxonomy annotation. Our work provides guidance for fully utilizing PE data of a marker gene when mergeable reads are limited.},
}

Asthma/microbiology
Bacteria/genetics
Child
Cluster Analysis
Genetic Markers
High-Throughput Nucleotide Sequencing/*methods
Humans
Metagenome
Metagenomics/methods
Microbiota/genetics
*Phylogeny
Sequence Analysis, DNA/*methods

@article {pmid32164527,
year = {2020},
author = {Kobus, R and Abuín, JM and Müller, A and Hellmann, SL and Pichel, JC and Pena, TF and Hildebrandt, A and Hankeln, T and Schmidt, B},
title = {A big data approach to metagenomics for all-food-sequencing.},
journal = {BMC bioinformatics},
volume = {21},
number = {1},
pages = {102},
pmid = {32164527},
issn = {1471-2105},
support = {HySim//Deutsche Forschungsgemeinschaft/ ; RTI2018-093336-B-C21//Ministerio de Econom?a y Competitividad/ ; ED481B 2018/013 and ED431C 2018/19//Xunta de Galicia/ ; 2816503814//Federal O?ce for Agriculture and Food/ ; },
mesh = {*Big Data ; Biosurveillance ; Food Analysis/*methods ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Software ; Whole Genome Sequencing/*methods ; },
abstract = {BACKGROUND: All-Food-Sequencing (AFS) is an untargeted metagenomic sequencing method that allows for the detection and quantification of food ingredients including animals, plants, and microbiota. While this approach avoids some of the shortcomings of targeted PCR-based methods, it requires the comparison of sequence reads to large collections of reference genomes. The steadily increasing amount of available reference genomes establishes the need for efficient big data approaches.

RESULTS: We introduce an alignment-free k-mer based method for detection and quantification of species composition in food and other complex biological matters. It is orders-of-magnitude faster than our previous alignment-based AFS pipeline. In comparison to the established tools CLARK, Kraken2, and Kraken2+Bracken it is superior in terms of false-positive rate and quantification accuracy. Furthermore, the usage of an efficient database partitioning scheme allows for the processing of massive collections of reference genomes with reduced memory requirements on a workstation (AFS-MetaCache) or on a Spark-based compute cluster (MetaCacheSpark).

CONCLUSIONS: We present a fast yet accurate screening method for whole genome shotgun sequencing-based biosurveillance applications such as food testing. By relying on a big data approach it can scale efficiently towards large-scale collections of complex eukaryotic and bacterial reference genomes. AFS-MetaCache and MetaCacheSpark are suitable tools for broad-scale metagenomic screening applications. They are available at https://muellan.github.io/metacache/afs.html (C++ version for a workstation) and https://github.com/jmabuin/MetaCacheSpark (Spark version for big data clusters).},
}

*Big Data
Biosurveillance
Food Analysis/*methods
Genome, Bacterial
High-Throughput Nucleotide Sequencing/*methods
Metagenome
Metagenomics/*methods
Microbiota/genetics
Software
Whole Genome Sequencing/*methods

@article {pmid31993987,
year = {2020},
author = {Farukh, M},
title = {Comparative genomic analysis of selenium utilization traits in different marine environments.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {58},
number = {2},
pages = {113-122},
doi = {10.1007/s12275-020-9250-0},
pmid = {31993987},
issn = {1976-3794},
mesh = {Ecosystem ; Genes, Bacterial/genetics ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; *Oceans and Seas ; Phosphotransferases/*genetics ; Proteobacteria/metabolism ; Selenium/metabolism ; },
abstract = {Selenium (Se) is an essential trace element for many organisms, which is required in the biosynthesis of proteins with selenocysteine, tRNAs with selenouridine, and certain enzymes with Se as a cofactor. Recent large-scale metagenomics projects provide a unique opportunity for studying the global trends of Se utilization in marine environments. Here, we analyzed samples from different marine microbial communities, revealed by the Tara Oceans project, to characterize the Se utilization traits. We found that the selenophosphate synthetase gene, which defines the overall Se utilization, and Se utilization traits are present in all samples. Regions with samples rich and poor in Se utilization traits were categorized. From the analysis of environmental factors, the mesopelagic zone and high temperature (> 15°C) of water are favorable, while geographical location has little influence on Se utilization. All Se utilization traits showed a relatively independent occurrence. The taxonomic classification of Se traits shows that most of the sequences corresponding to Se utilization traits belong to the phylum Proteobacteria. Overall, our study provides useful insights into the general features of Se utilization in ocean samples and may help to understand the evolutionary dynamics of Se utilization in different marine environments.},
}

Ecosystem
Genes, Bacterial/genetics
*Metagenome
Metagenomics
Microbiota/*genetics
*Oceans and Seas
Phosphotransferases/*genetics
Proteobacteria/metabolism
Selenium/metabolism

@article {pmid31866425,
year = {2020},
author = {Liu, Q and Liu, Q and Meng, H and Lv, H and Liu, Y and Liu, J and Wang, H and He, L and Qin, J and Wang, Y and Dai, Y and Otto, M and Li, M},
title = {Staphylococcus epidermidis Contributes to Healthy Maturation of the Nasal Microbiome by Stimulating Antimicrobial Peptide Production.},
journal = {Cell host & microbe},
volume = {27},
number = {1},
pages = {68-78.e5},
doi = {10.1016/j.chom.2019.11.003},
pmid = {31866425},
issn = {1934-6069},
support = {ZIA AI000904/AI/NIAID NIH HHS/United States ; },
mesh = {Adult ; Aged, 80 and over ; Antimicrobial Cationic Peptides/*biosynthesis ; Biofilms/growth & development ; Cell Line ; Child ; Child, Preschool ; Epidermal Cells ; Female ; High-Throughput Nucleotide Sequencing ; Host Microbial Interactions ; Humans ; Immunity, Innate ; Male ; Metagenomics ; Microbiota/*immunology ; Nasal Cavity/*microbiology ; RNA, Ribosomal, 16S ; *Staphylococcus epidermidis/isolation & purification/metabolism ; Symbiosis ; Young Adult ; },
abstract = {The composition of the human microbiome profoundly impacts human well-being. However, the mechanisms underlying microbiome maturation are poorly understood. The nasal microbiome is of particular importance as a source of many respiratory infections. Here, we performed a large sequencing and culture-based analysis of the human nasal microbiota from different age groups. We observed a significant decline of pathogenic bacteria before adulthood, with an increase of the commensal Staphylococcus epidermidis. In seniors, this effect was partially reversed. In vitro, many S. epidermidis isolates stimulated nasal epithelia to produce antimicrobial peptides, killing pathogenic competitors, while S. epidermidis itself proved highly resistant owing to its exceptional capacity to form biofilms. Furthermore, S. epidermidis isolates with high antimicrobial peptide-inducing and biofilm-forming capacities outcompeted pathogenic bacteria during nasal colonization in vivo. Our study identifies a pivotal role of S. epidermidis in healthy maturation of the nasal microbiome, which is achieved at least in part by symbiotic cooperation with innate host defense.},
}

Adult
Aged, 80 and over
Antimicrobial Cationic Peptides/*biosynthesis
Biofilms/growth & development
Cell Line
Child
Child, Preschool
Epidermal Cells
Female
High-Throughput Nucleotide Sequencing
Host Microbial Interactions
Humans
Immunity, Innate
Male
Metagenomics
Microbiota/*immunology
Nasal Cavity/*microbiology
RNA, Ribosomal, 16S
*Staphylococcus epidermidis/isolation & purification/metabolism
Symbiosis
Young Adult

@article {pmid31793046,
year = {2020},
author = {Liu, G and Chen, F and Cai, Y and Chen, Z and Luan, Q and Yu, X},
title = {Measuring the subgingival microbiota in periodontitis patients: Comparison of the surface layer and the underlying layers.},
journal = {Microbiology and immunology},
volume = {64},
number = {2},
pages = {99-112},
doi = {10.1111/1348-0421.12759},
pmid = {31793046},
issn = {1348-0421},
support = {81470740//National Natural Science Foundation of China/ ; },
mesh = {Actinobacteria/classification/genetics/isolation & purification ; Actinomyces/isolation & purification ; Adult ; Bacteria/classification/genetics/*isolation & purification ; Classification ; Dental Plaque/*microbiology ; Female ; Fusobacteria/classification/genetics/isolation & purification ; Fusobacterium/isolation & purification ; Fusobacterium nucleatum/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Metagenomics ; *Microbiota/genetics ; Periodontitis/*microbiology ; Phylogeny ; Porphyromonas gingivalis/isolation & purification ; Prevotella intermedia/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Spirochaetales/classification/genetics/isolation & purification ; Streptococcus intermedius/isolation & purification ; Treponema/isolation & purification ; Young Adult ; },
abstract = {Periodontitis is a major cause of tooth loss in adults that initially results from dental plaque. Subgingival plaque pathogenesis is affected by both community composition and plaque structures, although limited data are available concerning the latter. To bridge this knowledge gap, subgingival plaques were obtained using filter paper (the fourth layer) and curette (the first-third layers) sequentially and the phylogenetic differences between the first-third layers and the fourth layer were characterized by sequencing the V3-V4 regions of 16S rRNA. A total of 11 phyla, 148 genera, and 308 species were obtained by bioinformatic analysis, and no significant differences between the operational taxonomic unit numbers were observed for these groups. In both groups, the most abundant species were Porphyromonas gingivalis and Fusobacterium nucleatum. Actinomyces naeslundii, Streptococcus intermedius, and Prevotella intermedia possessed relatively high proportions in the first-third layers; while in the fourth layer, both traditional pathogens (Treponema denticola and Campylobacter rectus) and novel pathobionts (Eubacterium saphenum, Filifactor alocis, Treponema sp. HOT238) were prominent. Network analysis showed that either of them exhibited a scale-free property and was constructed by two negatively correlated components (the pathogen component and the nonpathogen component), while the synergy in the nonpathogen component was lower in the first-third layers than that in the fourth layer. After merging these two parts into a whole plaque group, the negative/positive correlation ratio increased. With potential connections, the first-third layers and the fourth layer showed characteristic key nodes in bacterial networks.},
}

Actinobacteria/classification/genetics/isolation & purification
Actinomyces/isolation & purification
Adult
Bacteria/classification/genetics/*isolation & purification
Classification
Dental Plaque/*microbiology
Female
Fusobacteria/classification/genetics/isolation & purification
Fusobacterium/isolation & purification
Fusobacterium nucleatum/isolation & purification
High-Throughput Nucleotide Sequencing/methods
Humans
Male
Metagenomics
*Microbiota/genetics
Periodontitis/*microbiology
Phylogeny
Porphyromonas gingivalis/isolation & purification
Prevotella intermedia/isolation & purification
RNA, Ribosomal, 16S/genetics
Spirochaetales/classification/genetics/isolation & purification
Streptococcus intermedius/isolation & purification
Treponema/isolation & purification
Young Adult

@article {pmid31672892,
year = {2019},
author = {Carrión, VJ and Perez-Jaramillo, J and Cordovez, V and Tracanna, V and de Hollander, M and Ruiz-Buck, D and Mendes, LW and van Ijcken, WFJ and Gomez-Exposito, R and Elsayed, SS and Mohanraju, P and Arifah, A and van der Oost, J and Paulson, JN and Mendes, R and van Wezel, GP and Medema, MH and Raaijmakers, JM},
title = {Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome.},
journal = {Science (New York, N.Y.)},
volume = {366},
number = {6465},
pages = {606-612},
doi = {10.1126/science.aaw9285},
pmid = {31672892},
issn = {1095-9203},
mesh = {Bacteria/classification ; Bacterial Physiological Phenomena ; Bacteroidetes/physiology ; Beta vulgaris/*microbiology ; Biodiversity ; Chitinases/genetics ; Disease Resistance ; Endophytes/*physiology ; Flavobacterium/physiology ; Genes, Bacterial ; Genome, Bacterial ; Metagenome ; *Microbiota ; Mutagenesis, Site-Directed ; Peptide Synthases/genetics ; Plant Diseases/*microbiology ; Plant Roots/*microbiology ; Polyketide Synthases/genetics ; Rhizoctonia/*pathogenicity ; Soil Microbiology ; },
abstract = {Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.},
}

Bacteria/classification
Bacterial Physiological Phenomena
Bacteroidetes/physiology
Beta vulgaris/*microbiology
Biodiversity
Chitinases/genetics
Disease Resistance
Endophytes/*physiology
Flavobacterium/physiology
Genes, Bacterial
Genome, Bacterial
Metagenome
*Microbiota
Mutagenesis, Site-Directed
Peptide Synthases/genetics
Plant Diseases/*microbiology
Plant Roots/*microbiology
Polyketide Synthases/genetics
Rhizoctonia/*pathogenicity
Soil Microbiology

@article {pmid31639050,
year = {2019},
author = {Zhou, G and Jiang, JY and Ju, CJ and Wang, W},
title = {Prediction of microbial communities for urban metagenomics using neural network approach.},
journal = {Human genomics},
volume = {13},
number = {Suppl 1},
pages = {47},
pmid = {31639050},
issn = {1479-7364},
support = {R01 GM115833/GM/NIGMS NIH HHS/United States ; },
mesh = {Algorithms ; Boston ; Cities ; Databases, Genetic ; Metagenomics/*methods ; Microbiota/*genetics ; Models, Genetic ; *Neural Networks, Computer ; New York ; Reproducibility of Results ; },
abstract = {BACKGROUND: Microbes are greatly associated with human health and disease, especially in densely populated cities. It is essential to understand the microbial ecosystem in an urban environment for cities to monitor the transmission of infectious diseases and detect potentially urgent threats. To achieve this goal, the DNA sample collection and analysis have been conducted at subway stations in major cities. However, city-scale sampling with the fine-grained geo-spatial resolution is expensive and laborious. In this paper, we introduce MetaMLAnn, a neural network based approach to infer microbial communities at unsampled locations given information reflecting different factors, including subway line networks, sampling material types, and microbial composition patterns.

RESULTS: We evaluate the effectiveness of MetaMLAnn based on the public metagenomics dataset collected from multiple locations in the New York and Boston subway systems. The experimental results suggest that MetaMLAnn consistently performs better than other five conventional classifiers under different taxonomic ranks. At genus level, MetaMLAnn can achieve F1 scores of 0.63 and 0.72 on the New York and the Boston datasets, respectively.

CONCLUSIONS: By exploiting heterogeneous features, MetaMLAnn captures the hidden interactions between microbial compositions and the urban environment, which enables precise predictions of microbial communities at unmeasured locations.},
}

Algorithms
Boston
Cities
Databases, Genetic
Metagenomics/*methods
Microbiota/*genetics
Models, Genetic
*Neural Networks, Computer
New York
Reproducibility of Results

@article {pmid31694288,
year = {2019},
author = {Castelán-Sánchez, HG and Elorrieta, P and Romoacca, P and Liñan-Torres, A and Sierra, JL and Vera, I and Batista-García, RA and Tenorio-Salgado, S and Lizama-Uc, G and Pérez-Rueda, E and Quispe-Ricalde, MA and Dávila-Ramos, S},
title = {Intermediate-Salinity Systems at High Altitudes in the Peruvian Andes Unveil a High Diversity and Abundance of Bacteria and Viruses.},
journal = {Genes},
volume = {10},
number = {11},
pages = {},
pmid = {31694288},
issn = {2073-4425},
mesh = {Actinobacteria/genetics ; Altitude ; Archaea/genetics ; Bacteria/genetics ; Bacteroidetes/genetics ; Biodiversity ; Euryarchaeota/genetics ; Metagenomics/*methods ; Microbiota/*genetics/*physiology ; Peru ; Phylogeny ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Salinity ; Salt Tolerance/*genetics ; Viruses/genetics ; },
abstract = {Intermediate-salinity environments are distributed around the world. Here, we present a snapshot characterization of two Peruvian thalassohaline environments at high altitude, Maras and Acos, which provide an excellent opportunity to increase our understanding of these ecosystems. The main goal of this study was to assess the structure and functional diversity of the communities of microorganisms in an intermediate-salinity environment, and we used a metagenomic shotgun approach for this analysis. These Andean hypersaline systems exhibited high bacterial diversity and abundance of the phyla Proteobacteria, Bacteroidetes, Balneolaeota, and Actinobacteria; in contrast, Archaea from the phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota were identified in low abundance. Acos harbored a more diverse prokaryotic community and a higher number of unique species compared with Maras. In addition, we obtained the draft genomes of two bacteria, Halomonas elongata and Idiomarina loihiensis, as well as the viral genomes of Enterobacteria lambda-like phage and Halomonas elongata-like phage and 27 partial novel viral halophilic genomes. The functional metagenome annotation showed a high abundance of sequences associated with detoxification, DNA repair, cell wall and capsule formation, and nucleotide metabolism; sequences for these functions were overexpressed mainly in bacteria and also in some archaea and viruses. Thus, their metabolic profiles afford a decrease in oxidative stress as well as the assimilation of nitrogen, a critical energy source for survival. Our work represents the first microbial characterization of a community structure in samples collected from Peruvian hypersaline systems.},
}

Actinobacteria/genetics
Altitude
Archaea/genetics
Bacteria/genetics
Bacteroidetes/genetics
Biodiversity
Euryarchaeota/genetics
Metagenomics/*methods
Microbiota/*genetics/*physiology
Peru
Phylogeny
Proteobacteria/genetics
RNA, Ribosomal, 16S/genetics
Salinity
Salt Tolerance/*genetics
Viruses/genetics

@article {pmid31651219,
year = {2019},
author = {Ahmed, N and Mahmoud, NF and Solyman, S and Hanora, A},
title = {Human Nasal Microbiome as Characterized by Metagenomics Differs Markedly Between Rural and Industrial Communities in Egypt.},
journal = {Omics : a journal of integrative biology},
volume = {23},
number = {11},
pages = {573-582},
doi = {10.1089/omi.2019.0144},
pmid = {31651219},
issn = {1557-8100},
mesh = {Bacteria/classification/genetics ; Biodiversity ; DNA Barcoding, Taxonomic ; Egypt ; Humans ; Industry ; *Metagenomics/methods ; *Microbiota ; Nasal Mucosa/*microbiology ; *Occupational Exposure ; Public Health Surveillance ; RNA, Ribosomal, 16S ; *Rural Population ; },
abstract = {Microbial communities residing in the nose play important roles in human health and disease. We report marked differences in nasal microbiota between a rural community and an industrial setting located near a major urban city. Nasal samples were collected from 19 healthy male subjects: 9 samples from persons living in a rural village, and 10 samples from ceramic factory workers in a major industrial Egyptian city. The nasal microbiota in the rural sample had higher and distinct diversity compared with industrial samples from workers exposed to pollution daily. Taxonomic analysis of the sequences revealed five major phyla; among these phyla were Actinobacteria, Proteobacteria, Bacteroidetes, and Fusobacteria, revealing significant abundance variation by geographical location. For example, the rural group had a significant increase in representation of Actinobacteria and Bacteroidetes (p = 0.004, p = 0.01, respectively) compared with the industrial group. However, the industrial group showed a significant increase in relative abundance of phylum Proteobacteria (p = 0.02). The most predominant genera for the rural group were Corynebacterium, Staphylococcus, Alloiococcus, and Peptoniphilus. By contrast, the industrial group was dominated by Staphylococcus, Sphingomonas, and Moraxella. Environmental pollution might alter the nasal microbiome leading to an attendant disturbance in the microbiome community structure. The clinical and public health implications of these nasal microbiome variations by rural and industrialized geography warrant further research. This study contributes to our knowledge of the bacterial composition of nasal microbiome in rural and industrialized geographies, and informs public health, respiratory medicine, and occupational health scholarship.},
}

Bacteria/classification/genetics
Biodiversity
DNA Barcoding, Taxonomic
Egypt
Humans
Industry
*Metagenomics/methods
*Microbiota
Nasal Mucosa/*microbiology
*Occupational Exposure
Public Health Surveillance
RNA, Ribosomal, 16S
*Rural Population

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

Adult
Age Factors
Biomarkers
DNA Barcoding, Taxonomic
Diabetes Mellitus/*epidemiology/*etiology
Egypt
Female
*Gastrointestinal Microbiome
High-Throughput Nucleotide Sequencing
Humans
Male
Metagenomics/methods
Middle Aged
Obesity/*epidemiology/*etiology
RNA, Ribosomal, 16S/genetics

@article {pmid31342640,
year = {2019},
author = {Maestre-Carballa, L and Lluesma Gomez, M and Angla Navarro, A and Garcia-Heredia, I and Martinez-Hernandez, F and Martinez-Garcia, M},
title = {Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome: bacteria, viruses and vesicles matter.},
journal = {Environmental microbiology},
volume = {21},
number = {12},
pages = {4582-4596},
doi = {10.1111/1462-2920.14758},
pmid = {31342640},
issn = {1462-2920},
support = {ACIF/2015/332//Generalitat Valenciana/International ; ACOM/2015/133//Generalitat Valenciana/International ; 5334//Gordon and Betty Moore Foundation/International ; RTI2018-094248-B-I00//Ministerio de Ciencia e Innovación/International ; },
mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/genetics ; *Drug Resistance, Microbial ; *Extracellular Vesicles ; Genes, Bacterial ; Metagenome ; Microbiota/*drug effects ; Viruses/genetics ; Waste Water/*microbiology ; *Water Microbiology ; },
abstract = {Wastewater treatment plants effluents are considered as hotspots for the dispersion of antibiotic resistance genes (ARGs) into natural ecosystems. The bacterial resistome (ARG collection in a metagenome) analyses have provided clues on antibacterial resistance dynamics. However, viruses and vesicles are frequently ignored. Here, we addressed the bacterial, viral and vesicle resistomes from a representative wastewater effluent in natural conditions and amended with polymyxin, which is used as a last resort antibiotic. Metagenomics showed that the natural prokaryotic resistome was vast (9000 ARG hits/Gb metagenome) and diverse, while viral resistome was two orders of magnitude lower (50 ARG hits/Gb metagenome) suggesting that viruses rarely encoded ARGs. After polymyxin amendment, data showed no ARG enrichment - including to polymyxin - in the microbiome. Remarkably, microbiomes responded to polymyxin with a vast release of putative vesicles (threefold increase compared with the control), which might be used as 'traps' to decrease the antibiotic concentration. Intriguingly, although polymyxin resistance genes (PRGs) were rare in the microbiome (0.018% of total ARG found), in the viral and vesicle fractions, PRGs were more abundant (0.5%-0.8% of total ARG found). Our data suggest that vesicles could have a more active role in the context of transmission of antibiotic resistances.},
}

Anti-Bacterial Agents/*pharmacology
Bacteria/drug effects/genetics
*Drug Resistance, Microbial
*Extracellular Vesicles
Genes, Bacterial
Metagenome
Microbiota/*drug effects
Viruses/genetics
Waste Water/*microbiology
*Water Microbiology

@article {pmid30997495,
year = {2019},
author = {Hornung, BVH and Zwittink, RD and Kuijper, EJ},
title = {Issues and current standards of controls in microbiome research.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {5},
pages = {},
pmid = {30997495},
issn = {1574-6941},
mesh = {Humans ; *Microbiota ; Reproducibility of Results ; Research/*standards ; },
abstract = {Good scientific practice is important in all areas of science. In recent years this has gained more and more attention, especially considering the 'scientific reproducibility crisis'. While most researchers are aware of the issues with good scientific practice, not all of these issues are necessarily clear, and the details can be very complicated. For many years it has been accepted to perform and publish sequencing based microbiome studies without including proper controls. Although in recent years more scientists realize the necessity of implementing controls, this poses a problem due to the complexity of the field. Another concern is the inability to properly interpret the information gained from controls in microbiome studies. Here, we will discuss these issues and provide a comprehensive overview of problematic points regarding controls in microbiome research, and of the current standards in this area.},
}

Humans
*Microbiota
Reproducibility of Results
Research/*standards

@article {pmid31087616,
year = {2019},
author = {Martin-Cuadrado, AB and Senel, E and Martínez-García, M and Cifuentes, A and Santos, F and Almansa, C and Moreno-Paz, M and Blanco, Y and García-Villadangos, M and Del Cura, MÁG and Sanz-Montero, ME and Rodríguez-Aranda, JP and Rosselló-Móra, R and Antón, J and Parro, V},
title = {Prokaryotic and viral community of the sulfate-rich crust from Peñahueca ephemeral lake, an astrobiology analogue.},
journal = {Environmental microbiology},
volume = {21},
number = {10},
pages = {3577-3600},
doi = {10.1111/1462-2920.14680},
pmid = {31087616},
issn = {1462-2920},
support = {ESP2015-69540-R//European Regional Development Fund/International ; AYA2011-24803//European Regional Development Fund/International ; CGL2015-66455-R//Spanish Ministry of Economy/International ; CLG2015_66686-C3-3//Spanish Ministry of Economy/International ; CLG2015_66686-C3-1//Spanish Ministry of Economy/International ; },
mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Biodiversity ; Exobiology ; Lakes/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride/metabolism ; Spain ; Sulfates/metabolism ; Viruses/classification/*genetics ; },
abstract = {Peñahueca is an athalassohaline hypersaline inland ephemeral lake originated under semiarid conditions in the central Iberian Peninsula (Spain). Its chemical composition makes it extreme for microbial life as well as a terrestrial analogue of other planetary environments. To investigate the persistence of microbial life associated with sulfate-rich crusts, we applied cultivation-independent methods (optical and electron microscopy, 16S rRNA gene profiling and metagenomics) to describe the prokaryotic community and its associated viruses. The diversity for Bacteria was very low and was vastly dominated by endospore formers related to Pontibacillus marinus of the Firmicutes phylum. The archaeal assemblage was more diverse and included taxa related to those normally found in hypersaline environments. Several 'metagenome assembled genomes' were recovered, corresponding to new species of Pontibacillus, several species from the Halobacteria and one new member of the Nanohaloarchaeota. The viral assemblage, although composed of the morphotypes typical of high salt systems, showed little similarity to previously isolated/reconstructed halophages. Several putative prophages of Pontibacillus and haloarchaeal hosts were identified. Remarkably, the Peñahueca sulfate-rich metagenome contained CRISPR-associated proteins and repetitions which were over 10-fold higher than in most hypersaline systems analysed so far.},
}

Archaea/classification/*genetics
Bacteria/classification/*genetics
Biodiversity
Exobiology
Lakes/*microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics
Sodium Chloride/metabolism
Spain
Sulfates/metabolism
Viruses/classification/*genetics

@article {pmid32391909,
year = {2020},
author = {Cuadrat, RRC and Sorokina, M and Andrade, BG and Goris, T and Dávila, AMR},
title = {Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples.},
journal = {GigaScience},
volume = {9},
number = {5},
pages = {},
doi = {10.1093/gigascience/giaa046},
pmid = {32391909},
issn = {2047-217X},
abstract = {BACKGROUND: The rise of antibiotic resistance (AR) in clinical settings is of great concern. Therefore, the understanding of AR mechanisms, evolution, and global distribution is a priority for patient survival. Despite all efforts in the elucidation of AR mechanisms in clinical strains, little is known about its prevalence and evolution in environmental microorganisms. We used 293 metagenomic samples from the TARA Oceans project to detect and quantify environmental antibiotic resistance genes (ARGs) using machine learning tools.

RESULTS: After manual curation of ARGs, their abundance and distribution in the global ocean are presented. Additionally, the potential of horizontal ARG transfer by plasmids and their correlation with environmental and geographical parameters is shown. A total of 99,205 environmental open reading frames (ORFs) were classified as 1 of 560 different ARGs conferring resistance to 26 antibiotic classes. We found 24,567 ORFs in putative plasmid sequences, suggesting the importance of mobile genetic elements in the dynamics of environmental ARG transmission. Moreover, 4,804 contigs with >=2 putative ARGs were found, including 2 plasmid-like contigs with 5 different ARGs, highlighting the potential presence of multi-resistant microorganisms in the natural ocean environment. Finally, we identified ARGs conferring resistance to some of the most relevant clinical antibiotics, revealing the presence of 15 ARGs similar to mobilized colistin resistance genes (mcr) with high abundance on polar biomes. Of these, 5 are assigned to Psychrobacter, a genus including opportunistic human pathogens.

CONCLUSIONS: This study uncovers the diversity and abundance of ARGs in the global ocean metagenome. Our results are available on Zenodo in MySQL database dump format, and all the code used for the analyses, including a Jupyter notebook js avaliable on Github. We also developed a dashboard web application (http://www.resistomedb.com) for data visualization.},
}

@article {pmid31823916,
year = {2019},
author = {Singh, S and Verma, N and Taneja, N},
title = {The human gut resistome: Current concepts & future prospects.},
journal = {The Indian journal of medical research},
volume = {150},
number = {4},
pages = {345-358},
pmid = {31823916},
issn = {0971-5916},
mesh = {Databases, Genetic ; Drug Resistance, Microbial/*genetics ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; },
abstract = {The human gut is home to a myriad of organisms. While some are harmless commensals, others are transient, pathogenic flora. The gut microbiome is composed of diverse bacterial flora, and apart from playing a major role in protecting from various infectious and non-infectious diseases, it plays an important role in resistance to antimicrobials. The collection of genes or genetic material that confers antimicrobial resistance constitutes the gut resistome, and it may involve the pathogens or commensals of the intestinal tract. The diversity of this gut resistome is influenced by various environmental factors including the diet and antibiotic exposure. This review highlights the recent concepts pertaining to the human gut resistome, factors affecting it, how it impacts human health and diseases, methods to study the resistome and potential therapeutic approaches.},
}

Databases, Genetic
Drug Resistance, Microbial/*genetics
*Gastrointestinal Microbiome
Humans
Metagenomics

@article {pmid31660953,
year = {2019},
author = {Garmaeva, S and Sinha, T and Kurilshikov, A and Fu, J and Wijmenga, C and Zhernakova, A},
title = {Studying the gut virome in the metagenomic era: challenges and perspectives.},
journal = {BMC biology},
volume = {17},
number = {1},
pages = {84},
pmid = {31660953},
issn = {1741-7007},
mesh = {Bacteriophages/*physiology ; Gastrointestinal Microbiome/*physiology ; Humans ; *Metagenome ; Metagenomics ; },
abstract = {The human gut harbors a complex ecosystem of microorganisms, including bacteria and viruses. With the rise of next-generation sequencing technologies, we have seen a quantum leap in the study of human-gut-inhabiting bacteria, yet the viruses that infect these bacteria, known as bacteriophages, remain underexplored. In this review, we focus on what is known about the role of bacteriophages in human health and the technical challenges involved in studying the gut virome, of which they are a major component. Lastly, we discuss what can be learned from studies of bacteriophages in other ecosystems.},
}

Bacteriophages/*physiology
Gastrointestinal Microbiome/*physiology
Humans
*Metagenome
Metagenomics

@article {pmid30897248,
year = {2019},
author = {Alrafas, HR and Busbee, PB and Nagarkatti, M and Nagarkatti, PS},
title = {Resveratrol modulates the gut microbiota to prevent murine colitis development through induction of Tregs and suppression of Th17 cells.},
journal = {Journal of leukocyte biology},
volume = {106},
number = {2},
pages = {467-480},
pmid = {30897248},
issn = {1938-3673},
support = {R01 AI129788/AI/NIAID NIH HHS/United States ; R01 MH094755/MH/NIMH NIH HHS/United States ; P20 GM103641/GM/NIGMS NIH HHS/United States ; P01 AT003961/AT/NCCIH NIH HHS/United States ; R01 AT006888/AT/NCCIH NIH HHS/United States ; R01 AI123947/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Anti-Inflammatory Agents, Non-Steroidal/*pharmacology ; Biomarkers ; Colitis/*etiology/metabolism/pathology/prevention & control ; Colonoscopy ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Female ; Gastrointestinal Microbiome/*drug effects/*immunology ; Humans ; Immunomodulation/*drug effects ; Metagenomics/methods ; Mice ; Resveratrol/*pharmacology ; T-Lymphocyte Subsets/immunology/metabolism ; T-Lymphocytes, Regulatory/drug effects/*immunology/metabolism ; Th17 Cells/drug effects/*immunology/metabolism ; },
abstract = {Inflammatory diseases of the gastrointestinal tract are often associated with microbial dysbiosis. Thus, dietary interactions with intestinal microbiota, to maintain homeostasis, play a crucial role in regulation of clinical disorders such as colitis. In the current study, we investigated if resveratrol, a polyphenol found in a variety of foods and beverages, would reverse microbial dysbiosis induced during colitis. Administration of resveratrol attenuated colonic inflammation and clinical symptoms in the murine model of 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced colitis. Resveratrol treatment in mice with colitis led to an increase in CD4+ FOXP3+ and CD4+ IL-10+ T cells, and a decrease in CD4+ IFN-γ+ and CD4+ IL-17+ T cells. 16S rRNA gene sequencing to investigate alterations in the gut microbiota revealed that TNBS caused significant dysbiosis, which was reversed following resveratrol treatment. Analysis of cecal flush revealed that TNBS administration led to an increase in species such as Bacteroides acidifaciens, but decrease in species such as Ruminococcus gnavus and Akkermansia mucinphilia, as well as a decrease in SCFA i-butyric acid. However, resveratrol treatment restored the gut bacteria back to homeostatic levels, and increased production of i-butyric acid. Fecal transfer experiments confirmed the protective role of resveratrol-induced microbiota against colitis inasmuch as such recipient mice were more resistant to TNBS-colitis and exhibited polarization toward CD4+ FOXP3+ T cells and decreases in CD4+ IFN-γ+ and CD4+ IL-17+ T cells. Collectively, these data demonstrate that resveratrol-mediated attenuation of colitis results from reversal of microbial dysbiosis induced during colitis and such microbiota protect the host from colonic inflammation by inducing Tregs while suppressing inflammatory Th1/Th17 cells.},
}

Animals
Anti-Inflammatory Agents, Non-Steroidal/*pharmacology
Biomarkers
Colitis/*etiology/metabolism/pathology/prevention & control
Colonoscopy
Disease Models, Animal
Fecal Microbiota Transplantation
Female
Gastrointestinal Microbiome/*drug effects/*immunology
Humans
Immunomodulation/*drug effects
Metagenomics/methods
Mice
Resveratrol/*pharmacology
T-Lymphocyte Subsets/immunology/metabolism
T-Lymphocytes, Regulatory/drug effects/*immunology/metabolism
Th17 Cells/drug effects/*immunology/metabolism

@article {pmid32380596,
year = {2019},
author = {Francini-Filho, RB and Cordeiro, MC and Omachi, CY and Rocha, AM and Bahiense, L and Garcia, GD and Tschoeke, D and de Almeida, MG and Rangel, TP and De Oliveira, BCV and de Almeida, DQR and Menezes, R and Mazzei, EF and Joyeux, JC and Rezende, CE and Thompson, CC and Thompson, FL},
title = {Remote sensing, isotopic composition and metagenomics analyses revealed Doce River ore plume reached the southern Abrolhos Bank Reefs.},
journal = {The Science of the total environment},
volume = {697},
number = {},
pages = {134038},
doi = {10.1016/j.scitotenv.2019.134038},
pmid = {32380596},
issn = {1879-1026},
abstract = {On November 5th, 2015, the Fundão dam rupture released >50 million m3 of ore tailings into the Doce River, Minas Gerais State, Brazil. The huge volume of mud spread along the river and reached the sea, 17 days after the disaster, in Regência, Espírito Santo State (ES). In 2018, after three years of the disaster, the impacts of the ore tailings in the marine environment are still unclear. This study aims to investigate possible short-term impacts in marine biodiversity caused by the ore tailings' mud over the reef ecosystems that are closest to the disaster area: i.e. recently discovered reefs in the southern Abrolhos Bank. A remote sensing surveillance including winds, sea surface temperature, total suspended material and watercolor (MODIS Aqua data) indicated that the iron tailings plume reached the southern portion of Abrolhos Bank on June 16th, 2016. Subsequently, to obtain further evidence of the presence of the tailings in the coral reefs, water samples were collected in a gradient spanning from the river estuary to the reefs in southern Abrolhos Bank, we also analyzed the isotopic and microbial composition of the samples, as well as the reef benthic composition. Despite no clues of negative impact on benthic (coral) communities, isotopic analysis confirmed the presence of the plume over the reefs area. This study serves as a baseline for future long-term impact assessments of the health of coral reefs in the Abrolhos Bank.},
}

@article {pmid31269412,
year = {2019},
author = {Zhang, F and Yang, R},
title = {Life history and functional capacity of the microbiome are altered in beta-cypermethrin-resistant cockroaches.},
journal = {International journal for parasitology},
volume = {49},
number = {9},
pages = {715-723},
doi = {10.1016/j.ijpara.2019.04.006},
pmid = {31269412},
issn = {1879-0135},
mesh = {Animals ; Bacteria/classification/genetics ; Blattellidae/*drug effects/genetics/growth & development/microbiology ; Computational Biology ; DNA, Bacterial/chemistry/isolation & purification ; Female ; Genotype ; Insecticide Resistance/genetics ; Insecticides/*pharmacology ; Male ; Metagenome/genetics ; Microbiota/drug effects/*physiology ; Nymph/growth & development ; Pyrethrins/*pharmacology ; RNA, Ribosomal, 16S/chemistry ; },
abstract = {Cockroaches are widely perceived to evolve resistance to insecticides. Over-expression of a resistance-conferring gene can be costly and may require energy and resource reallocation for metabolic and developmental processes. To evaluate whether changes in the composition of gut microbiota in Blattella germanica affected its resistance evolution to beta-cypermethrin and to determine the role of gut microbiota in host growth and development, we studied the relationship between insecticide resistance and the diversity and genetic content of gut microbiota in cockroaches. Results suggest beta-cypermethrin-resistant cockroaches (R strain) exhibited a delayed development period and reduced adult longevity compared with susceptible cockroaches (S strain). Based on 16S rRNA gene sequencing and community metagenomics, we found that the relative abundance of Lactobacillus and Acetobacteraceae were significantly lower in the R strain compared with the S strain in the foregut and midgut of both strains. Functional annotation of Kyoto Encyclopedia of Genes and Genomes (KEGG) modules of midgut genes in the two strains revealed that 10.6% were involved in metabolism, while the relative abundance in the R strain was 7.4%. Unigenes were also translated into amino acid sequences and assigned to protein families based on hits to the Carbohydrate-Active enzymes (CAZy) database. This process identified the glycoside hydrolases, glycosyl transferases and carbohydrate-binding modules of the S strain as all being significantly higher in diversity than those in the R strain. Overall, we conclude that fitness-related costs increased in the resistant strain of cockroaches compared with the susceptible strain, and the variation in insect gut microbiota, especially those related to growth and development, was an important influencing factor.},
}

Animals
Bacteria/classification/genetics
Blattellidae/*drug effects/genetics/growth & development/microbiology
Computational Biology
DNA, Bacterial/chemistry/isolation & purification
Female
Genotype
Insecticide Resistance/genetics
Insecticides/*pharmacology
Male
Metagenome/genetics
Microbiota/drug effects/*physiology
Nymph/growth & development
Pyrethrins/*pharmacology
RNA, Ribosomal, 16S/chemistry

@article {pmid30649283,
year = {2019},
author = {Sickel, W and Van de Weyer, AL and Bemm, F and Schultz, J and Keller, A},
title = {Venus flytrap microbiotas withstand harsh conditions during prey digestion.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {3},
pages = {},
doi = {10.1093/femsec/fiz010},
pmid = {30649283},
issn = {1574-6941},
mesh = {Amino Acids/pharmacology ; Animals ; Droseraceae/*microbiology ; Host Microbial Interactions ; Indenes/pharmacology ; Metagenomics ; *Microbiota/drug effects/genetics ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The carnivorous Venus flytrap (Dionaea muscipula) overcomes environmental nutrient limitation by capturing small animals. Such prey is digested with an acidic enzyme-containing mucilage that is secreted into the closed trap. However, surprisingly little is known about associations with microorganisms. Therefore, we assessed microbiotas of traps and petioles for the Venus flytrap by 16S amplicon meta-barcoding. We also performed time-series assessments of dynamics during digestion in traps and experimental acidification of petioles. We found that the traps hosted distinct microbiotas that differed from adjacent petioles. Further, they showed a significant taxonomic turnover during digestion. Following successful catches, prey-associated bacteria had strong effects on overall composition. With proceeding digestion, however, microbiotas were restored to compositions resembling pre-digestion stages. A comparable, yet less extensive shift was found when stimulating digestion with coronatine. Artificial acidification of petioles did not induce changes towards trap-like communities. Our results show that trap microbiota were maintained during digestion despite harsh conditions and recovered after short-term disturbances through prey microbiota. This indicates trap-specific and resilient associations. By mapping to known genomes, we predicted putative adaptations and functional implications for the system, yet direct mechanisms and quantification of host benefits, like the involvement in digestion, remain to be addressed.},
}

Amino Acids/pharmacology
Animals
Droseraceae/*microbiology
Host Microbial Interactions
Indenes/pharmacology
Metagenomics
*Microbiota/drug effects/genetics
Plant Leaves/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid30203066,
year = {2019},
author = {Biderre-Petit, C and Taib, N and Gardon, H and Hochart, C and Debroas, D},
title = {New insights into the pelagic microorganisms involved in the methane cycle in the meromictic Lake Pavin through metagenomics.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {3},
pages = {},
doi = {10.1093/femsec/fiy183},
pmid = {30203066},
issn = {1574-6941},
mesh = {Hydrogen/metabolism ; Lakes/chemistry/*microbiology ; Metabolic Networks and Pathways/genetics ; Metagenome ; Metagenomics ; Methane/*metabolism ; Microbiota/*genetics ; Nitrogen/metabolism ; Plankton/classification/genetics/isolation & purification/metabolism ; *Water Microbiology ; },
abstract = {Advances in metagenomics have given rise to the possibility of obtaining genome sequences from uncultured microorganisms, even for those poorly represented in the microbial community, thereby providing an important means to study their ecology and evolution. In this study, metagenomic sequencing was carried out at four sampling depths having different oxygen concentrations or environmental conditions in the water column of Lake Pavin. By analyzing the sequenced reads and matching the contigs to the proxy genomes of the closest cultivated relatives, we evaluated the metabolic potential of the dominant planktonic species involved in the methane cycle. We demonstrated that methane-producing communities were dominated by the genus Methanoregula while methane-consuming communities were dominated by the genus Methylobacter, thus confirming prior observations. Our work allowed the reconstruction of a draft of their core metabolic pathways. Hydrogenotrophs, the genes required for acetate activation in the methanogen genome, were also detected. Regarding methanotrophy, Methylobacter was present in the same areas as the non-methanotrophic, methylotrophic Methylotenera, which could suggest a relationship between these two groups. Furthermore, the presence of a large gene inventory for nitrogen metabolism (nitrate transport, denitrification, nitrite assimilation and nitrogen fixation, for instance) was detected in the Methylobacter genome.},
}

Hydrogen/metabolism
Lakes/chemistry/*microbiology
Metabolic Networks and Pathways/genetics
Metagenome
Metagenomics
Methane/*metabolism
Microbiota/*genetics
Nitrogen/metabolism
Plankton/classification/genetics/isolation & purification/metabolism
*Water Microbiology

@article {pmid31370880,
year = {2019},
author = {Minot, SS and Willis, AD},
title = {Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {110},
pmid = {31370880},
issn = {2049-2618},
mesh = {Bacteria/classification ; Cluster Analysis ; Colorectal Neoplasms/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*microbiology ; *Metagenome ; Metagenomics ; Reproducibility of Results ; Sequence Analysis, DNA ; Whole Genome Sequencing ; },
abstract = {BACKGROUND: Whole-genome "shotgun" (WGS) metagenomic sequencing is an increasingly widely used tool for analyzing the metagenomic content of microbiome samples. While WGS data contains gene-level information, it can be challenging to analyze the millions of microbial genes which are typically found in microbiome experiments. To mitigate the ultrahigh dimensionality challenge of gene-level metagenomics, it has been proposed to cluster genes by co-abundance to form Co-Abundant Gene groups (CAGs). However, exhaustive co-abundance clustering of millions of microbial genes across thousands of biological samples has previously been intractable purely due to the computational challenge of performing trillions of pairwise comparisons.

RESULTS: Here we present a novel computational approach to the analysis of WGS datasets in which microbial gene groups are the fundamental unit of analysis. We use the Approximate Nearest Neighbor heuristic for near-exhaustive average linkage clustering to group millions of genes by co-abundance. This results in thousands of high-quality CAGs representing complete and partial microbial genomes. We applied this method to publicly available WGS microbiome surveys and found that the resulting microbial CAGs associated with inflammatory bowel disease (IBD) and colorectal cancer (CRC) were highly reproducible and could be validated independently using multiple independent cohorts.

CONCLUSIONS: This powerful approach to gene-level metagenomics provides a powerful path forward for identifying the biological links between the microbiome and human health. By proposing a new computational approach for handling high dimensional metagenomics data, we identified specific microbial gene groups that are associated with disease that can be used to identify strains of interest for further preclinical and mechanistic experimentation.},
}

Bacteria/classification
Cluster Analysis
Colorectal Neoplasms/*microbiology
*Gastrointestinal Microbiome
Humans
Inflammatory Bowel Diseases/*microbiology
*Metagenome
Metagenomics
Reproducibility of Results
Sequence Analysis, DNA
Whole Genome Sequencing

@article {pmid31279340,
year = {2019},
author = {Velsko, IM and Fellows Yates, JA and Aron, F and Hagan, RW and Frantz, LAF and Loe, L and Martinez, JBR and Chaves, E and Gosden, C and Larson, G and Warinner, C},
title = {Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {102},
pmid = {31279340},
issn = {2049-2618},
mesh = {Bacteria/*classification ; *Bacterial Physiological Phenomena ; Bacterial Proteins/genetics ; Biofilms/*growth & development ; Bone and Bones/microbiology ; DNA, Ancient/analysis ; DNA, Bacterial/genetics ; Dental Calculus/history/*microbiology ; Dental Plaque/*microbiology ; Female ; History, Ancient ; Humans ; Male ; Metagenomics ; Microbiota/*physiology ; Periodontal Diseases/microbiology ; Proteomics ; Tooth/*microbiology ; },
abstract = {BACKGROUND: Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates.

RESULTS: Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins.

CONCLUSIONS: Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.},
}

Bacteria/*classification
*Bacterial Physiological Phenomena
Bacterial Proteins/genetics
Biofilms/*growth & development
Bone and Bones/microbiology
DNA, Ancient/analysis
DNA, Bacterial/genetics
Dental Calculus/history/*microbiology
Dental Plaque/*microbiology
Female
History, Ancient
Humans
Male
Metagenomics
Microbiota/*physiology
Periodontal Diseases/microbiology
Proteomics
Tooth/*microbiology

@article {pmid31248462,
year = {2019},
author = {Marathe, NP and Berglund, F and Razavi, M and Pal, C and Dröge, J and Samant, S and Kristiansson, E and Larsson, DGJ},
title = {Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {97},
pmid = {31248462},
issn = {2049-2618},
mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Bacterial Proteins/*genetics ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; *Hospitals ; Humans ; India ; Integrons/*genetics ; Metagenomics ; Microbial Sensitivity Tests ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; beta-Lactamases/*genetics ; },
abstract = {BACKGROUND: Hospital wastewaters contain fecal material from a large number of individuals, of which many are undergoing antibiotic therapy. It is, thus, plausible that hospital wastewaters could provide opportunities to find novel carbapenemases and other resistance genes not yet described in clinical strains. Our aim was therefore to investigate the microbiota and antibiotic resistome of hospital effluent collected from the city of Mumbai, India, with a special focus on identifying novel carbapenemases.

RESULTS: Shotgun metagenomics revealed a total of 112 different mobile antibiotic resistance gene types, conferring resistance against almost all classes of antibiotics. Beta-lactamase genes, including encoding clinically important carbapenemases, such as NDM, VIM, IMP, KPC, and OXA-48, were abundant. NDM (0.9% relative abundance to 16S rRNA genes) was the most common carbapenemase gene, followed by OXA-58 (0.84% relative abundance to 16S rRNA genes). Among the investigated mobile genetic elements, class 1 integrons (11% relative abundance to 16S rRNA genes) were the most abundant. The genus Acinetobacter accounted for as many as 30% of the total 16S rRNA reads, with A. baumannii accounting for an estimated 2.5%. High throughput sequencing of amplified integron gene cassettes identified a novel functional variant of an IMP-type (proposed IMP-81) carbapenemase gene (eight aa substitutions) along with recently described novel resistance genes like sul4 and blaRSA1. Using a computational hidden Markov model, we detected 27 unique metallo-beta-lactamase (MBL) genes in the shotgun data, of which nine were novel subclass B1 genes, one novel subclass B2, and 10 novel subclass B3 genes. Six of the seven novel MBL genes were functional when expressed in Escherichia coli.

CONCLUSION: By exploring hospital wastewater from India, our understanding of the diversity of carbapenemases has been extended. The study also demonstrates that the microbiota of hospital wastewater can serve as a reservoir of novel resistance genes, including previously uncharacterized carbapenemases with the potential to spread further.},
}

Anti-Bacterial Agents/pharmacology
Bacteria/drug effects/genetics
Bacterial Proteins/*genetics
Drug Resistance, Microbial/*genetics
*Genes, Bacterial
*Hospitals
Humans
India
Integrons/*genetics
Metagenomics
Microbial Sensitivity Tests
Microbiota/*genetics
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Sewage/*microbiology
beta-Lactamases/*genetics

@article {pmid32015529,
year = {2020},
author = {Dion, MB and Oechslin, F and Moineau, S},
title = {Phage diversity, genomics and phylogeny.},
journal = {Nature reviews. Microbiology},
volume = {18},
number = {3},
pages = {125-138},
doi = {10.1038/s41579-019-0311-5},
pmid = {32015529},
issn = {1740-1534},
mesh = {Bacteriophages/*classification/*genetics/ultrastructure ; *Biodiversity ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Viral ; Host Microbial Interactions ; Metagenomics ; *Phylogeny ; Recombination, Genetic ; Viral Proteins/genetics ; Virion/ultrastructure ; },
abstract = {Recent advances in viral metagenomics have enabled the rapid discovery of an unprecedented catalogue of phages in numerous environments, from the human gut to the deep ocean. Although these advances have expanded our understanding of phage genomic diversity, they also revealed that we have only scratched the surface in the discovery of novel viruses. Yet, despite the remarkable diversity of phages at the nucleotide sequence level, the structural proteins that form viral particles show strong similarities and conservation. Phages are uniquely interconnected from an evolutionary perspective and undergo multiple events of genetic exchange in response to the selective pressure of their hosts, which drives their diversity. In this Review, we explore phage diversity at the structural, genomic and community levels as well as the complex evolutionary relationships between phages, moulded by the mosaicity of their genomes.},
}

Bacteriophages/*classification/*genetics/ultrastructure
*Biodiversity
Evolution, Molecular
Gene Transfer, Horizontal
*Genome, Viral
Host Microbial Interactions
Metagenomics
*Phylogeny
Recombination, Genetic
Viral Proteins/genetics
Virion/ultrastructure

@article {pmid31818246,
year = {2019},
author = {Shelomi, M and Lin, SS and Liu, LY},
title = {Transcriptome and microbiome of coconut rhinoceros beetle (Oryctes rhinoceros) larvae.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {957},
pmid = {31818246},
issn = {1471-2164},
support = {MOST 106-2311-B-002-002-MY3//Ministry of Science and Technology (TW)/ ; MOST 108-2313-B-002-050//Ministry of Science and Technology, Taiwan/ ; MOST 108-2311-B-002-018-MY3//Ministry of Science and Technology, Taiwan/ ; },
mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Coleoptera/*genetics/*microbiology ; Female ; Gastrointestinal Tract/metabolism/microbiology ; Gene Expression ; Insect Proteins/genetics ; Isoptera/microbiology ; Larva/genetics/microbiology ; Male ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; Transcriptome ; },
abstract = {BACKGROUND: The coconut rhinoceros beetle, Oryctes rhinoceros, is a major pest of palm crops in tropical Asia and the Pacific Islands. Little molecular data exists for this pest, impeding our ability to develop effective countermeasures and deal with the species' growing resistance to viral biocontrols. We present the first molecular biology analyses of this species, including a metagenomic assay to understand the microbiome of different sections of its digestive tract, and a transcriptomics assay to complement the microbiome data and to shed light on genes of interest like plant cell wall degrading enzymes and immunity and xenobiotic resistance genes.

RESULTS: The gut microbiota of Oryctes rhinoceros larvae is quite similar to that of the termite gut, as both species feed on decaying wood. We found the first evidence for endogenous beta-1,4-endoglucanase in the beetle, plus evidence for microbial cellobiase, suggesting the beetle can degrade cellulose together with its gut microfauna. A number of antimicrobial peptides are expressed, particularly by the fat body but also by the midgut and hindgut.

CONCLUSIONS: This transcriptome provides a wealth of data about the species' defense against chemical and biological threats, has uncovered several potentially new species of microbial symbionts, and significantly expands our knowledge about this pest.},
}

Animals
Bacteria/classification/genetics/isolation & purification
Coleoptera/*genetics/*microbiology
Female
Gastrointestinal Tract/metabolism/microbiology
Gene Expression
Insect Proteins/genetics
Isoptera/microbiology
Larva/genetics/microbiology
Male
Metagenomics
*Microbiota/genetics
Phylogeny
Transcriptome

@article {pmid31775777,
year = {2019},
author = {Yang, L and Haidar, G and Zia, H and Nettles, R and Qin, S and Wang, X and Shah, F and Rapport, SF and Charalampous, T and Methé, B and Fitch, A and Morris, A and McVerry, BJ and O'Grady, J and Kitsios, GD},
title = {Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study.},
journal = {Respiratory research},
volume = {20},
number = {1},
pages = {265},
pmid = {31775777},
issn = {1465-993X},
support = {U01 HL098962/HL/NHLBI NIH HHS/United States ; R01 HL097376/HL/NHLBI NIH HHS/United States ; MR/N013956/1//UK Antimicrobial Resistance Cross Council Initiative/ ; K23 HL139987/HL/NHLBI NIH HHS/United States ; MR/N013956/1/MRC_/Medical Research Council/United Kingdom ; K24 HL123342/HL/NHLBI NIH HHS/United States ; BBS/E/F/000PR10348/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RP-PG-0514-20018/DH_/Department of Health/United Kingdom ; BBS/E/F/000PR10349/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RP-PG-0514-20018//National Institute for Health Research/ ; K23 GM122069/GM/NIGMS NIH HHS/United States ; A749//Rosetrees Trust/ ; P01 HL114453/HL/NHLBI NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/administration & dosage ; Case-Control Studies ; DNA, Bacterial/*genetics ; Feasibility Studies ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Metagenomics/methods ; Microbiota/*genetics ; *Nanopores ; Pneumonia/diagnosis/*genetics/*therapy ; Reference Values ; Respiration, Artificial/methods ; Respiratory Insufficiency/diagnosis/genetics/therapy ; Risk Factors ; Sensitivity and Specificity ; Severity of Illness Index ; Virulence Factors/genetics ; },
abstract = {BACKGROUND: Metagenomic sequencing of respiratory microbial communities for pathogen identification in pneumonia may help overcome the limitations of culture-based methods. We examined the feasibility and clinical validity of rapid-turnaround metagenomics with Nanopore™ sequencing of clinical respiratory specimens.

METHODS: We conducted a case-control study of mechanically-ventilated patients with pneumonia (nine culture-positive and five culture-negative) and without pneumonia (eight controls). We collected endotracheal aspirates and applied a microbial DNA enrichment method prior to metagenomic sequencing with the Oxford Nanopore MinION device. For reference, we compared Nanopore results against clinical microbiologic cultures and bacterial 16S rRNA gene sequencing.

RESULTS: Human DNA depletion enabled in depth sequencing of microbial communities. In culture-positive cases, Nanopore revealed communities with high abundance of the bacterial or fungal species isolated by cultures. In four cases with resistant clinical isolates, Nanopore detected antibiotic resistance genes corresponding to the phenotypic resistance in antibiograms. In culture-negative pneumonia, Nanopore revealed probable bacterial pathogens in 1/5 cases and Candida colonization in 3/5 cases. In controls, Nanopore showed high abundance of oral bacteria in 5/8 subjects, and identified colonizing respiratory pathogens in other subjects. Nanopore and 16S sequencing showed excellent concordance for the most abundant bacterial taxa.

CONCLUSIONS: We demonstrated technical feasibility and proof-of-concept clinical validity of Nanopore metagenomics for severe pneumonia diagnosis, with striking concordance with positive microbiologic cultures, and clinically actionable information obtained from sequencing in culture-negative samples. Prospective studies with real-time metagenomics are warranted to examine the impact on antimicrobial decision-making and clinical outcomes.},
}

Anti-Bacterial Agents/administration & dosage
Case-Control Studies
DNA, Bacterial/*genetics
Feasibility Studies
Female
High-Throughput Nucleotide Sequencing/methods
Humans
Male
Metagenomics/methods
Microbiota/*genetics
*Nanopores
Pneumonia/diagnosis/*genetics/*therapy
Reference Values
Respiration, Artificial/methods
Respiratory Insufficiency/diagnosis/genetics/therapy
Risk Factors
Sensitivity and Specificity
Severity of Illness Index
Virulence Factors/genetics

@article {pmid31662858,
year = {2019},
author = {Ungaro, F and Massimino, L and D'Alessio, S and Danese, S},
title = {The gut virome in inflammatory bowel disease pathogenesis: From metagenomics to novel therapeutic approaches.},
journal = {United European gastroenterology journal},
volume = {7},
number = {8},
pages = {999-1007},
pmid = {31662858},
issn = {2050-6406},
mesh = {Animals ; Bacteria/*classification ; Caliciviridae Infections/complications ; Computational Biology/methods ; Dysbiosis/*complications ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Inflammation/virology ; Inflammatory Bowel Diseases/*etiology/therapy/*virology ; Intestines/*virology ; Metagenomics/*methods ; Microbiota/genetics ; Models, Animal ; Molecular Targeted Therapy/methods ; Norovirus/genetics ; Phylogeny ; Viruses/genetics ; },
abstract = {The association of intestinal dysbiosis with the pathogenesis of inflammatory bowel disease has been well established. Besides bacteria, microbiota comprises yeasts, archaea, protists and viruses, neglected actors in inflammatory bowel disease-associated microbiota. In the past, a great limitation in studying microbiota composition was the low sensitivity of sequencing technologies and that few computational approaches were sufficient to thoroughly analyse the whole microbiome. However, new cutting-edge technologies in nucleic acid sequencing, -omics analysis and the innovative statistics and bioinformatics pipelines made possible more sensitive and accurate metagenomics, ultimately identifying novel players in intestinal inflammation, including prokaryotic and eukaryotic viruses, that together form the gut virome. The discovery of peculiar inflammatory bowel disease-associated microbial strains will not only shed new light on inflammatory bowel disease aetiogenesis, they may also support the development of novel therapeutic strategies not merely treating symptoms, but precisely counteracting the primary cause of chronic intestinal inflammation.},
}

Animals
Bacteria/*classification
Caliciviridae Infections/complications
Computational Biology/methods
Dysbiosis/*complications
High-Throughput Nucleotide Sequencing/methods
Humans
Inflammation/virology
Inflammatory Bowel Diseases/*etiology/therapy/*virology
Intestines/*virology
Metagenomics/*methods
Microbiota/genetics
Models, Animal
Molecular Targeted Therapy/methods
Norovirus/genetics
Phylogeny
Viruses/genetics

@article {pmid31657225,
year = {2020},
author = {Albhaisi, SAM and Bajaj, JS and Sanyal, AJ},
title = {Role of gut microbiota in liver disease.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {318},
number = {1},
pages = {G84-G98},
doi = {10.1152/ajpgi.00118.2019},
pmid = {31657225},
issn = {1522-1547},
mesh = {Animals ; Bacteria/metabolism/*pathogenicity ; Disease Progression ; Dysbiosis ; *Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Intestines/*microbiology ; Liver/*metabolism/pathology ; Liver Diseases/*metabolism/*microbiology/pathology ; Prognosis ; Risk Factors ; },
abstract = {The gut microbiome is the natural intestinal inhabitant that has been recognized recently as a major player in the maintenance of human health and the pathophysiology of many diseases. Those commensals produce metabolites that have various effects on host biological functions. Therefore, alterations in the normal composition or diversity of microbiome have been implicated in various diseases, including liver cirrhosis and nonalcoholic fatty liver disease. Moreover, accumulating evidence suggests that progression of dysbiosis can be associated with worsening of liver disease. Here, we review the possible roles for gut microbiota in the development, progression, and complication of liver disease.},
}

Animals
Bacteria/metabolism/*pathogenicity
Disease Progression
Dysbiosis
*Gastrointestinal Microbiome
Host-Pathogen Interactions
Humans
Intestines/*microbiology
Liver/*metabolism/pathology
Liver Diseases/*metabolism/*microbiology/pathology
Prognosis
Risk Factors

@article {pmid31573126,
year = {2019},
author = {Galambos, D and Anderson, RE and Reveillaud, J and Huber, JA},
title = {Genome-resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep-sea hydrothermal vents.},
journal = {Environmental microbiology},
volume = {21},
number = {11},
pages = {4395-4410},
pmid = {31573126},
issn = {1462-2920},
support = {//Alfred P. Sloan Foundation/International ; ASTEP NNX-327 09AB75G/NASA/NASA/United States ; Exobiology 80NSSC18K1076/NASA/NASA/United States ; OCE-1061863//National Science Foundation/International ; ASTEP NNX-327 09AB75G/NASA/NASA/United States ; Exobiology 80NSSC18K1076/NASA/NASA/United States ; },
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Hydrothermal Vents/*microbiology ; Metagenome ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; Transcriptome ; },
abstract = {The structure and function of microbial communities inhabiting the subseafloor near hydrothermal systems are influenced by fluid geochemistry, geologic setting and fluid flux between vent sites, as well as biological interactions. Here, we used genome-resolved metagenomics and metatranscriptomics to examine patterns of gene abundance and expression and assess potential niche differentiation in microbial communities in venting fluids from hydrothermal vent sites at the Mid-Cayman Rise. We observed similar patterns in gene and transcript abundance between two geochemically distinct vent fields at the community level but found that each vent site harbours a distinct microbial community with differing transcript abundances for individual microbial populations. Through an analysis of metabolic pathways in 64 metagenome-assembled genomes (MAGs), we show that MAG transcript abundance can be tied to differences in metabolic pathways and to potential metabolic interactions between microbial populations, allowing for niche-partitioning and divergence in both population distribution and activity. Our results illustrate that most microbial populations have a restricted distribution within the seafloor, and that the activity of those microbial populations is tied to both genome content and abiotic factors.},
}

Archaea/*genetics
Bacteria/*genetics
Hydrothermal Vents/*microbiology
Metagenome
Metagenomics
Microbiota/*genetics
Phylogeny
Transcriptome

@article {pmid31180804,
year = {2019},
author = {Mark Welch, JL and Dewhirst, FE and Borisy, GG},
title = {Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis.},
journal = {Annual review of microbiology},
volume = {73},
number = {},
pages = {335-358},
pmid = {31180804},
issn = {1545-3251},
support = {R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE024468/DE/NIDCR NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; Mouth/*microbiology ; Spatial Analysis ; },
abstract = {Microbial communities are complex and dynamic, composed of hundreds of taxa interacting across multiple spatial scales. Advances in sequencing and imaging technology have led to great strides in understanding both the composition and the spatial organization of these complex communities. In the human mouth, sequencing results indicate that distinct sites host microbial communities that not only are distinguishable but to a meaningful degree are composed of entirely different microbes. Imaging suggests that the spatial organization of these communities is also distinct. Together, the literature supports the idea that most oral microbes are site specialists. A clear understanding of microbiota structure at different sites in the mouth enables mechanistic studies, informs the generation of hypotheses, and strengthens the position of oral microbiology as a model system for microbial ecology in general.},
}

Humans
*Microbiota
Mouth/*microbiology
Spatial Analysis

@article {pmid30824335,
year = {2019},
author = {Davies, NK and O'Sullivan, JM and Plank, LD and Murphy, R},
title = {Altered gut microbiome after bariatric surgery and its association with metabolic benefits: A systematic review.},
journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery},
volume = {15},
number = {4},
pages = {656-665},
doi = {10.1016/j.soard.2019.01.033},
pmid = {30824335},
issn = {1878-7533},
mesh = {*Bariatric Surgery ; *Gastrointestinal Microbiome ; Humans ; *Obesity/physiopathology/surgery ; Treatment Outcome ; },
abstract = {Bariatric surgery is currently the recommended therapy for significant weight reduction and remission of type 2 diabetes. Different types of bariatric surgery result in dramatic changes to gut bacteria but the contribution of such changes to the metabolic benefits achieved is still unclear. This systematic review of 14 clinical studies, incorporating 222 participants (146 patients with Roux-en-Y gastric bypass, 25 with sleeve gastrectomy, 30 with biliointestinal bypass, 7 with vertical banded gastroplasty, and 14 with an adjustable gastric band) reveals generally increased microbial diversity and gene richness after surgery. Major species-level changes include a decrease in the relative abundance of Faecalibacterium prausnitzii and increase in Escherichia coli. Decreases in the relative abundance of Firmicutes after sleeve gastrectomy and increases in Bacteroidetes and Proteobacteria after Roux-en-Y gastric bypass were seen. Microbial changes after surgery are discussed in the context of potential confounding effects of baseline diet, medications, and type 2 diabetes, with recommendations to consider these factors in future studies, to identify potentially causal associations with observed metabolic benefits.},
}

*Bariatric Surgery
*Gastrointestinal Microbiome
Humans
*Obesity/physiopathology/surgery
Treatment Outcome

@article {pmid31744921,
year = {2019},
author = {Estrela, AB and Nakashige, TG and Lemetre, C and Woodworth, ID and Weisman, JL and Cohen, LJ and Brady, SF},
title = {Functional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors.},
journal = {mBio},
volume = {10},
number = {6},
pages = {},
pmid = {31744921},
issn = {2150-7511},
support = {R01 AT009562/AT/NCCIH NIH HHS/United States ; },
mesh = {Bacteria/*genetics ; Bacterial Infections/*metabolism/*microbiology ; Gene Expression Regulation, Bacterial ; Gene Library ; *Genome, Bacterial ; Humans ; *Metagenomics/methods ; Microbiota ; NF-kappa B/*metabolism ; Operon ; Phylogeny ; },
abstract = {The effect of the microbiota on its human host is driven, at least in part, by small-molecule and protein effectors it produces. Here, we report on the use of functional multigenomic screening to identify microbiota-encoded effectors. In this study, genomic DNA from 116 human-associated bacteria was cloned en masse, and the resulting multigenomic library was screened using a nuclear factor-κB reporter (NF-κB) assay. Functional multigenomics builds on the concept of functional metagenomics but takes advantage of increasing advances in cultivating and sequencing human-associated bacteria. Effector genes found to confer NF-κB-inducing activity to Escherichia coli encode proteins in four general categories: cell wall hydrolases, membrane transporters, lipopolysaccharide biosynthetic enzymes, and proteins of unknown function. The compact nature of multigenomic libraries, which results from the ability to normalize input DNA ratios, should simplify screening of libraries using diverse heterologous hosts and reporter assays, increasing the rate of discovery of novel effector genes.IMPORTANCE Human-associated bacteria are thought to encode bioactive small molecules and proteins that play an intimate role in human health and disease. Here, we report on the creation and functional screening of a multigenomic library constructed using genomic DNA from 116 bacteria found at diverse sites across the human body. Individual clones were screened for genes capable of conferring NF-κB-inducing activity to Escherichia coli NF-κB is a useful reporter for a range of cellular processes related to immunity, pathogenesis, and inflammation. Compared to the screening of metagenomic libraries, the ability to normalize input DNA ratios when constructing a multigenomic library should facilitate the more efficient examination of commensal bacteria for diverse bioactivities. Multigenomic screening takes advantage of the growing available resources in culturing and sequencing the human microbiota and generates starting points for more in-depth studies on the mechanisms by which commensal bacteria interact with their human host.},
}

Bacteria/*genetics
Bacterial Infections/*metabolism/*microbiology
Gene Expression Regulation, Bacterial
Gene Library
*Genome, Bacterial
Humans
*Metagenomics/methods
Microbiota
NF-kappa B/*metabolism
Operon
Phylogeny

@article {pmid31316785,
year = {2019},
author = {Gutin, L and Piceno, Y and Fadrosh, D and Lynch, K and Zydek, M and Kassam, Z and LaMere, B and Terdiman, J and Ma, A and Somsouk, M and Lynch, S and El-Nachef, N},
title = {Fecal microbiota transplant for Crohn disease: A study evaluating safety, efficacy, and microbiome profile.},
journal = {United European gastroenterology journal},
volume = {7},
number = {6},
pages = {807-814},
pmid = {31316785},
issn = {2050-6406},
mesh = {Adolescent ; Adult ; Aged ; Crohn Disease/etiology/*therapy ; *Fecal Microbiota Transplantation/adverse effects/methods ; Female ; Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; Young Adult ; },
abstract = {Background: Emerging trials suggest fecal microbiota transplantation (FMT) is a promising treatment for ulcerative colitis; however, there is a paucity of data in Crohn disease (CD).

Objective: The objectives of this article are to determine whether single-dose FMT improves clinical and endoscopic outcomes in CD patients and to identify meaningful changes in the microbiome in response to FMT.

Methods: We performed a prospective, open-label, single-center study. Ten CD patients underwent FMT and were evaluated for clinical response (defined as decrease in Harvey-Bradshaw Index score ≥3 at one month post-FMT) and microbiome profile (16S ribosomal RNA sequencing) at one month post-FMT.

Results: Three of 10 patients responded to FMT. Two of 10 patients had significant adverse events requiring escalation of therapy. On microbiome analysis, bacterial communities of responders had increased relative abundance of bacteria commonly found in donor gut microbiota.

Conclusions: Single-dose FMT in this cohort of CD patients showed modest effect and potential for harm. Responders tended to have lower baseline alpha diversity, suggesting baseline perturbation of microbiota may be an indicator of potential responders to FMT in this patient population. Controlled trials are needed to further assess the efficacy and safety of FMT in CD and determine whether FMT is a viable option in this patient population.Clinicaltrials.gov number: NCT02460705.},
}

Adolescent
Adult
Aged
Crohn Disease/etiology/*therapy
*Fecal Microbiota Transplantation/adverse effects/methods
Female
Gastrointestinal Microbiome
Humans
Male
Metagenomics/methods
Middle Aged
RNA, Ribosomal, 16S/genetics
Treatment Outcome
Young Adult

@article {pmid31393213,
year = {2019},
author = {ElRakaiby, MT and Gamal-Eldin, S and Amin, MA and Aziz, RK},
title = {Hospital Microbiome Variations As Analyzed by High-Throughput Sequencing.},
journal = {Omics : a journal of integrative biology},
volume = {23},
number = {9},
pages = {426-438},
doi = {10.1089/omi.2019.0111},
pmid = {31393213},
issn = {1557-8100},
mesh = {Anti-Bacterial Agents/pharmacology ; Computational Biology/methods ; Cross Infection/epidemiology/microbiology ; Drug Resistance, Bacterial ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing ; *Hospitals/standards ; Humans ; *Metagenome ; *Metagenomics/methods ; Microbial Sensitivity Tests ; *Microbiota ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; United States ; },
abstract = {Hospital-acquired infections remain a serious threat to human life and are becoming a top public health issue. As the latest advances in sequencing technologies have allowed the unbiased identification of bacterial communities, we aimed to implement emerging omics technologies to characterize a hospital's microbiome at the center of Cairo, Egypt. To this end, we screened surfaces and inanimate objects in the hospital, focusing on bed sheets and door knobs, with additional screening for resistant microbes and resistance genes. While bacterial load and community composition were not dramatically different between door knobs of hospital units with different hygiene levels, the bacterial communities on door knob samples were richer and more diverse than those detected on bed sheets. Bacteria detected on door knobs were a mix of those associated with dust/particulate matter/debris (e.g., Bacillus, Geobacillus, Aeribacillus) and skin-associated bacteria (e.g., Staphylococcus, Corynebacterium). The latter were among the core genera shared by all analyzed samples. Conversely, bacteria that were more abundant in bed sheets were not associated with a particular source (e.g., Pseudomonas and Nitrobacter). Resistance screening indicated an expansion of a mobile beta-lactamase-encoding gene (blaTEM), reflecting its current global spread. This study is a first step toward more comprehensive screening of hospital surfaces and correlating their microbiome with hospital outbreaks or chronic infections. We conclude that, as hospitals are unique built environments, these findings can inform future infection control strategies in hospitals and health care-related built environments, and attest to the importance of the emerging hospital microbiome research field.},
}

Anti-Bacterial Agents/pharmacology
Computational Biology/methods
Cross Infection/epidemiology/microbiology
Drug Resistance, Bacterial
*Environmental Microbiology
High-Throughput Nucleotide Sequencing
*Hospitals/standards
Humans
*Metagenome
*Metagenomics/methods
Microbial Sensitivity Tests
*Microbiota
Pilot Projects
RNA, Ribosomal, 16S/genetics
Reproducibility of Results
United States

@article {pmid31320306,
year = {2019},
author = {Carissimi, C and Laudadio, I and Palone, F and Fulci, V and Cesi, V and Cardona, F and Alfonsi, C and Cucchiara, S and Isoldi, S and Stronati, L},
title = {Functional analysis of gut microbiota and immunoinflammation in children with autism spectrum disorders.},
journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver},
volume = {51},
number = {10},
pages = {1366-1374},
doi = {10.1016/j.dld.2019.06.006},
pmid = {31320306},
issn = {1878-3562},
mesh = {Autism Spectrum Disorder/immunology/*microbiology/physiopathology ; Case-Control Studies ; Child ; Child Development ; Child, Preschool ; Comorbidity ; Cytokines/blood ; Escherichia coli/isolation & purification ; Feces/microbiology ; Female ; Gastrointestinal Diseases/*immunology ; *Gastrointestinal Microbiome ; Humans ; *Inflammation ; Male ; Phenylpropionates/metabolism ; },
abstract = {BACKGROUND AND AIMS: Recent evidence implicates gut microbiota (GM) and immune alterations in autism spectrum disorders (ASD). We assess GM profile and peripheral levels of immunological, neuronal and bacterial molecules in ASD children and controls. Alarmin HMGB1 was explored as a non-invasive biomarker to monitor gastrointestinal (GI) symptoms.

METHODS: Thirty ASD children and 14 controls entered into the study. GM metagenomic analysis was performed for 16 ASD patients and 7 controls. GM functional profile was assessed by GO term analysis. Blood levels of IL-1β, TNFα, TGFβ, IL-10, INFγ, IL-8, lipopolysaccharide, Neurotensin, Sortilin1 and GSSG/GSH ratio were analyzed in all subjects by ELISA. Fecal HMGB1 was analyzed by Western blot.

RESULTS: We observed a significant decrease in bacterial diversity. Furthermore, 82 GO terms underrepresented in ASD. Four of them pointed at 3,3 phenylpropionate catabolism and were imputable to Escherichia coli (E. coli) group. Serum levels of TNFα, TGFβ, NT, and SORT-1 increased in ASD patients. Fecal levels of HMGB1 correlated with GI sign severity in ASD children.

CONCLUSIONS: We suggest that a decrease of E. coli might affect the propionate catabolism in ASD. We report occurrence of peripheral inflammation in ASD children. We propose fecal HMGB1 as a non-invasive biomarker to detect GI symptoms.},
}

Autism Spectrum Disorder/immunology/*microbiology/physiopathology
Case-Control Studies
Child
Child Development
Child, Preschool
Comorbidity
Cytokines/blood
Escherichia coli/isolation & purification
Feces/microbiology
Female
Gastrointestinal Diseases/*immunology
*Gastrointestinal Microbiome
Humans
*Inflammation
Male
Phenylpropionates/metabolism

@article {pmid31188063,
year = {2019},
author = {Laudadio, I and Fulci, V and Stronati, L and Carissimi, C},
title = {Next-Generation Metagenomics: Methodological Challenges and Opportunities.},
journal = {Omics : a journal of integrative biology},
volume = {23},
number = {7},
pages = {327-333},
doi = {10.1089/omi.2019.0073},
pmid = {31188063},
issn = {1557-8100},
mesh = {Animals ; Big Data ; Biodiversity ; Computational Biology/methods ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiological Techniques ; Microbiology/trends ; Microbiota ; },
abstract = {Metagenomics is not only one of the newest omics system science technologies but also one that has arguably the broadest set of applications and impacts globally. Metagenomics has found vast utility not only in environmental sciences, ecology, and public health but also in clinical medicine and looking into the future, in planetary health. In line with the One Health concept, metagenomics solicits collaboration between molecular biologists, geneticists, microbiologists, clinicians, computational biologists, plant biologists, veterinarians, and other health care professionals. Almost every ecological niche of our planet hosts an extremely diverse community of organisms that are still poorly characterized. Detailed characterization of the features of such communities is instrumental to our comprehension of ecological, biological, and clinical complexity. This expert review article evaluates how metagenomics is improving our knowledge of microbiota composition from environmental to human samples. Furthermore, we offer an analysis of the common technical and methodological challenges and potential pitfalls arising from metagenomics approaches, such as metagenomics study design, data processing, and interpretation. All in all, at this critical juncture of further growth of the metagenomics field, it is time to critically reflect on the lessons learned and the future prospects of next-generation metagenomics science, technology, and conceivable applications, particularly from the standpoint of a metagenomics methodology perspective.},
}

Animals
Big Data
Biodiversity
Computational Biology/methods
Databases, Genetic
High-Throughput Nucleotide Sequencing/methods
Humans
Metagenome
Metagenomics/*methods
Microbiological Techniques
Microbiology/trends
Microbiota

@article {pmid31092280,
year = {2019},
author = {Heinken, A and Ravcheev, DA and Baldini, F and Heirendt, L and Fleming, RMT and Thiele, I},
title = {Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {75},
pmid = {31092280},
issn = {2049-2618},
mesh = {Bile Acids and Salts/*metabolism ; *Gastrointestinal Microbiome ; Genomics ; Host-Pathogen Interactions ; Humans ; Inflammatory Bowel Diseases/metabolism/*microbiology ; Lipid Metabolism ; Metagenomics ; *Systems Biology ; },
abstract = {BACKGROUND: The human gut microbiome performs important functions in human health and disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of primary bile acids and their subsequent deconjugation and transformation by the gut microbiome. To understand these system-level host-microbe interactions, a mechanistic, multi-scale computational systems biology approach that integrates the different types of omic data is needed. Here, we use a systematic workflow to computationally model bile acid metabolism in gut microbes and microbial communities.

RESULTS: Therefore, we first performed a comparative genomic analysis of bile acid deconjugation and biotransformation pathways in 693 human gut microbial genomes and expanded 232 curated genome-scale microbial metabolic reconstructions with the corresponding reactions (available at https://vmh.life). We then predicted the bile acid biotransformation potential of each microbe and in combination with other microbes. We found that each microbe could produce maximally six of the 13 secondary bile acids in silico, while microbial pairs could produce up to 12 bile acids, suggesting bile acid biotransformation being a microbial community task. To investigate the metabolic potential of a given microbiome, publicly available metagenomics data from healthy Western individuals, as well as inflammatory bowel disease patients and healthy controls, were mapped onto the genomes of the reconstructed strains. We constructed for each individual a large-scale personalized microbial community model that takes into account strain-level abundances. Using flux balance analysis, we found considerable variation in the potential to deconjugate and transform primary bile acids between the gut microbiomes of healthy individuals. Moreover, the microbiomes of pediatric inflammatory bowel disease patients were significantly depleted in their bile acid production potential compared with that of controls. The contributions of each strain to overall bile acid production potential across individuals were found to be distinct between inflammatory bowel disease patients and controls. Finally, bottlenecks limiting secondary bile acid production potential were identified in each microbiome model.

CONCLUSIONS: This large-scale modeling approach provides a novel way of analyzing metagenomics data to accelerate our understanding of the metabolic interactions between the host and gut microbiomes in health and diseases states. Our models and tools are freely available to the scientific community.},
}

Bile Acids and Salts/*metabolism
*Gastrointestinal Microbiome
Genomics
Host-Pathogen Interactions
Humans
Inflammatory Bowel Diseases/metabolism/*microbiology
Lipid Metabolism
Metagenomics
*Systems Biology

@article {pmid31078141,
year = {2019},
author = {Rocafort, M and Noguera-Julian, M and Rivera, J and Pastor, L and Guillén, Y and Langhorst, J and Parera, M and Mandomando, I and Carrillo, J and Urrea, V and Rodríguez, C and Casadellà, M and Calle, ML and Clotet, B and Blanco, J and Naniche, D and Paredes, R},
title = {Evolution of the gut microbiome following acute HIV-1 infection.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {73},
pmid = {31078141},
issn = {2049-2618},
mesh = {Acute Disease ; Adult ; Bacteria/*classification/isolation & purification ; CD4-Positive T-Lymphocytes ; CD8-Positive T-Lymphocytes ; Chronic Disease ; Feces/virology ; Female ; *Gastrointestinal Microbiome ; HIV Infections/drug therapy/*microbiology ; HIV-1/isolation & purification ; Humans ; Male ; Metagenomics ; Middle Aged ; Mozambique ; Prospective Studies ; *Transcriptome ; Viral Load ; Virus Shedding ; Young Adult ; },
abstract = {BACKGROUND: In rhesus macaques, simian immunodeficiency virus infection is followed by expansion of enteric viruses but has a limited impact on the gut bacteriome. To understand the longitudinal effects of HIV-1 infection on the human gut microbiota, we prospectively followed 49 Mozambican subjects diagnosed with recent HIV-1 infection (RHI) and 54 HIV-1-negative controls for 9-18 months and compared them with 98 chronically HIV-1-infected subjects treated with antiretrovirals (n = 27) or not (n = 71).

RESULTS: We show that RHI is followed by increased fecal adenovirus shedding, which persists during chronic HIV-1 infection and does not resolve with ART. Recent HIV-1 infection is also followed by transient non-HIV-specific changes in the gut bacterial richness and composition. Despite early resilience to change, an HIV-1-specific signature in the gut bacteriome-featuring depletion of Akkermansia, Anaerovibrio, Bifidobacterium, and Clostridium-previously associated with chronic inflammation, CD8+ T cell anergy, and metabolic disorders, can be eventually identified in chronically HIV-1-infected subjects.

CONCLUSIONS: Recent HIV-1 infection is associated with increased fecal shedding of eukaryotic viruses, transient loss of bacterial taxonomic richness, and long-term reductions in microbial gene richness. An HIV-1-associated microbiome signature only becomes evident in chronically HIV-1-infected subjects.},
}

Acute Disease
Adult
Bacteria/*classification/isolation & purification
CD4-Positive T-Lymphocytes
CD8-Positive T-Lymphocytes
Chronic Disease
Feces/virology
Female
*Gastrointestinal Microbiome
HIV Infections/drug therapy/*microbiology
HIV-1/isolation & purification
Humans
Male
Metagenomics
Middle Aged
Mozambique
Prospective Studies
*Transcriptome
Viral Load
Virus Shedding
Young Adult

@article {pmid31027515,
year = {2019},
author = {Kim, J and Guk, JH and Mun, SH and An, JU and Song, H and Kim, J and Ryu, S and Jeon, B and Cho, S},
title = {Metagenomic analysis of isolation methods of a targeted microbe, Campylobacter jejuni, from chicken feces with high microbial contamination.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {67},
pmid = {31027515},
issn = {2049-2618},
mesh = {Animals ; Bacteriological Techniques ; Campylobacter jejuni/*genetics/*isolation & purification ; Chickens/*microbiology ; Culture Media/chemistry ; Feces/*microbiology ; Metagenomics ; *Microbiota ; },
abstract = {BACKGROUND: Originating from poultry, particularly chickens, Campylobacter jejuni is the leading foodborne pathogen worldwide and a major cause of campylobacteriosis. Isolating C. jejuni is difficult due to its specific growth requirements, the presence of viable but non-culturable bacteria, and because it is often masked by competing flora. Currently, there is no optimized method for isolating C. jejuni from chicken feces. Here, we evaluated the method for isolating C. jejuni from chicken feces using culture-independent sequence-based metagenomics and culture-dependent tools. Further, we assessed changes in microbial communities during microbe isolation to determine how the process can be improved.

RESULTS: Fourteen different variations of C. jejuni isolation procedures were applied to all 35 chicken fecal samples. These variations included using different enrichment broths (without enrichment or enrichment in Bolton or Preston broth), different ratios of sample-to-enrichment broth (1:101, 1:102, and 1:103), and different selective agars (modified charcoal-cefoperazone-deoxycholate agar (mCCDA) or Preston agar). Enrichment during isolation of C. jejuni was evaluated on the basis of microbial diversity and taxonomic composition using metagenomics tools. The effect of selective media was evaluated using a combination of metagenomics and culture-dependent tools. Microbial diversity significantly decreased during the enrichment process, regardless of the type of enrichment broth, with the most significant decrease observed at a feces-to-broth ratio of 1:103. Particularly, in 103-Preston broth, the relative abundance of Campylobacter increased, while extended-spectrum beta-lactamase-producing Escherichia coli, which interfere with Campylobacter isolation, decreased. Metagenomics results were validated by quantitative PCR and culture-dependent analysis. Additionally, selective media affected the isolation results, although microbes with high relative abundance during enrichment were also frequently isolated using culture-dependent methods. Significantly more C. jejuni was isolated from mCCDA than from Preston agar enriched in 103 Preston broth.

CONCLUSIONS: Enrichment in Preston broth at a ratio of 1:103 followed by spreading onto mCCDA was the most effective method for isolating C. jejuni. This is the first study to apply metagenomics to evaluate a method for isolating a targeted microbe, C. jejuni, from chicken feces, a source with high microbial contamination. Thus, metagenomics can be applied to improve methods for isolating bacteria that are difficult to separate.},
}

Animals
Bacteriological Techniques
Campylobacter jejuni/*genetics/*isolation & purification
Chickens/*microbiology
Culture Media/chemistry
Feces/*microbiology
Metagenomics
*Microbiota

@article {pmid30995938,
year = {2019},
author = {Le Doujet, T and De Santi, C and Klemetsen, T and Hjerde, E and Willassen, NP and Haugen, P},
title = {Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua).},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {64},
pmid = {30995938},
issn = {2049-2618},
mesh = {*Animal Migration ; Animals ; DNA, Bacterial/genetics ; Female ; Gadus morhua/*microbiology ; *Gastrointestinal Microbiome ; Genetic Variation ; Genome, Bacterial ; Male ; *Metagenomics ; Norway ; Photobacterium/*classification ; Proteomics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The population of Atlantic cod (Gadus morhua), also known as Northeast Arctic cod, migrating Atlantic cod, or simply "skrei," lives mainly in the Barents Sea and Svalbard waters and migrates in annual cycles to the Norwegian coast in order to spawn eggs during late winter. It is the world's largest population of Atlantic cod, and the population is distinct from the Norwegian coastal cod (or "fjord" cod). Despite the biological, economic, and cultural importance of migrating Atlantic cod, current knowledge on the associated microbiota is very limited. Using shotgun metagenomics and metaproteomics approaches, we present here the gut microbiota, metagenome-assembled genomes (MAGs) of the most abundant bacterial species, DNA-based functional profile, and the metaproteome of Atlantic cod specimens caught at a spawning area in an open ocean outside of Tromsø, Norway.

RESULTS: Our analyses identified 268 bacterial families in DNA isolated from feces of 6 individual migrating Atlantic cod. The most abundant family was Vibrionaceae (52%; 83% if unclassified reads are excluded), with Photobacterium (genus) representing the vast majority. The recovery of metagenome-assembled genomes provided further details and suggests that several closely related Photobacterium strains from the Photobacterium phosphoreum clade are the most abundant. A genomic-based functional profiling showed that the most abundant functional subsystems are "Carbohydrates"; "Amino Acids and Derivatives"; "Protein Metabolism"; "Cofactors, Vitamins, Prosthetic, Groups, and Pigments"; and "DNA Metabolism," which is in agreement with other studies of gut microbiomes of marine organisms. Finally, the MS-based metaproteomic dataset revealed that the functional category "Protein Metabolism" is highly overrepresented (3×) when compared to the genome-based functional profile, which shows that ribosomal proteins are rich in the bacterial cytosol.

CONCLUSION: We present here the first study of bacterial diversity of the gut of migrating Atlantic cod using shotgun sequencing and metagenome-assembled genomes (MAGs). The most abundant bacteria belong to the Photobacterium genus (Vibrionaceae family). We also constructed functional profiles of the gut microbiome. These may be used in future studies as a platform for mining of commercially interesting cold-active enzymes.},
}

*Animal Migration
Animals
DNA, Bacterial/genetics
Female
Gadus morhua/*microbiology
*Gastrointestinal Microbiome
Genetic Variation
Genome, Bacterial
Male
*Metagenomics
Norway
Photobacterium/*classification
Proteomics
Sequence Analysis, DNA

@article {pmid32346574,
year = {2020},
author = {Ajilogba, CF and Babalola, OO},
title = {Bambara groundnut soil metagenomics data.},
journal = {Data in brief},
volume = {30},
number = {},
pages = {105542},
doi = {10.1016/j.dib.2020.105542},
pmid = {32346574},
issn = {2352-3409},
abstract = {Metagenomics analysis was carried out on extracted DNA of Rhizospheric soil samples from Bambara groundnut. This dataset presented reports on the bacterial communities at the different growth stages of Bambara groundnut and the bulk soil. Paired-end Illumina-Miseq sequencing of 16S rRNA genes was carried on the soil samples of the bacterial community with the phyla dominated by Actinobacteria (30.1%), Proteobacteria (22%), Acidobacteria (20.9%), Bacteroides (8.4%), Chloroflex (4.5%) and Firmicutes (4.4%) in all the soil samples. Samples from the bulk soil had the least average percent phyla, while samples at seed maturity stage had the highest average percent phyla. The alpha diversity at p = 0.05 was highest at this stage compared to the others and the control. Rubrobacter was the most predominant genera, after which is Acidobacterium and Skermanella. The biodiversity profile generated from the metagenomics analysis is useful in increasing knowledge of the drought-tolerance ability of Bambara groundnut. The data generated can be used to compare bacterial diversity at different growth stages of plants.},
}

@article {pmid32024572,
year = {2020},
author = {Newbold, CJ and Ramos-Morales, E},
title = {Review: Ruminal microbiome and microbial metabolome: effects of diet and ruminant host.},
journal = {Animal : an international journal of animal bioscience},
volume = {14},
number = {S1},
pages = {s78-s86},
doi = {10.1017/S1751731119003252},
pmid = {32024572},
issn = {1751-732X},
mesh = {Animals ; Diet/veterinary ; Fermentation ; *Gastrointestinal Microbiome ; Gene Expression Profiling/veterinary ; *Metabolome ; Metabolomics ; *Metagenome ; Metagenomics ; Methane/*metabolism ; Nitrogen/metabolism ; Phylogeny ; Plant Extracts/metabolism ; *Proteome ; Proteomics ; Rumen/metabolism ; Ruminants/metabolism/*microbiology ; *Transcriptome ; },
abstract = {The rumen contains a great diversity of prokaryotic and eukaryotic microorganisms that allow the ruminant to utilize ligno-cellulose material and to convert non-protein nitrogen into microbial protein to obtain energy and amino acids. However, rumen fermentation also has potential deleterious consequences associated with the emissions of greenhouse gases, excessive nitrogen excreted in manure and may also adversely influence the nutritional value of ruminant products. While several strategies for optimizing the energy and nitrogen use by ruminants have been suggested, a better understanding of the key microorganisms involved and their activities is essential to manipulate rumen processes successfully. Diet is the most obvious factor influencing the rumen microbiome and fermentation. Among dietary interventions, the ban of antimicrobial growth promoters in animal production systems has led to an increasing interest in the use of plant extracts to manipulate the rumen. Plant extracts (e.g. saponins, polyphenol compounds, essential oils) have shown potential to decrease methane emissions and improve the efficiency of nitrogen utilization; however, there are limitations such as inconsistency, transient and adverse effects for their use as feed additives for ruminants. It has been proved that the host animal may also influence the rumen microbial population both as a heritable trait and through the effect of early-life nutrition on microbial population structure and function in adult ruminants. Recent developments have allowed phylogenetic information to be upscaled to metabolic information; however, research effort on cultivation of microorganisms for an in-depth study and characterization is needed. The introduction and integration of metagenomic, transcriptomic, proteomic and metabolomic techniques is offering the greatest potential of reaching a truly systems-level understanding of the rumen; studies have been focused on the prokaryotic population and a broader approach needs to be considered.},
}

Animals
Diet/veterinary
Fermentation
*Gastrointestinal Microbiome
Gene Expression Profiling/veterinary
*Metabolome
Metabolomics
*Metagenome
Metagenomics
Methane/*metabolism
Nitrogen/metabolism
Phylogeny
Plant Extracts/metabolism
*Proteome
Proteomics
Rumen/metabolism
Ruminants/metabolism/*microbiology
*Transcriptome

@article {pmid31241822,
year = {2019},
author = {Santillan, E and Seshan, H and Constancias, F and Wuertz, S},
title = {Trait-based life-history strategies explain succession scenario for complex bacterial communities under varying disturbance.},
journal = {Environmental microbiology},
volume = {21},
number = {10},
pages = {3751-3764},
doi = {10.1111/1462-2920.14725},
pmid = {31241822},
issn = {1462-2920},
support = {//Ministry of Education/International ; //Singapore National Research Foundation/International ; },
mesh = {Bacteria/genetics/*growth & development ; Bioreactors ; Ecosystem ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S ; },
abstract = {Trait-based approaches are increasingly gaining importance in community ecology, as a way of finding general rules for the mechanisms driving changes in community structure and function under the influence of perturbations. Frameworks for life-history strategies have been successfully applied to describe changes in plant and animal communities upon disturbance. To evaluate their applicability to complex bacterial communities, we operated replicated wastewater treatment bioreactors for 35 days and subjected them to eight different disturbance frequencies of a toxic pollutant (3-chloroaniline), starting with a mixed inoculum from a full-scale treatment plant. Relevant ecosystem functions were tracked and microbial communities assessed through metagenomics and 16S rRNA gene sequencing. Combining a series of ordination, statistical and network analysis methods, we associated different life-history strategies with microbial communities across the disturbance range. These strategies were evaluated using tradeoffs in community function and genotypic potential, and changes in bacterial genus composition. We further compared our findings with other ecological studies and adopted a semi-quantitative competitors, stress-tolerants, ruderals (CSR) classification. The framework reduces complex data sets of microbial traits, functions and taxa into ecologically meaningful components to help understand the system response to disturbance and hence represents a promising tool for managing microbial communities.},
}

Bacteria/genetics/*growth & development
Bioreactors
Ecosystem
Metagenomics/methods
*Microbiota
RNA, Ribosomal, 16S

@article {pmid32341166,
year = {2020},
author = {Deboutte, W and Beller, L and Yinda, CK and Maes, P and de Graaf, DC and Matthijnssens, J},
title = {Honey-bee-associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1921859117},
pmid = {32341166},
issn = {1091-6490},
abstract = {Honey bees (Apis mellifera) produce an enormous economic value through their pollination activities and play a central role in the biodiversity of entire ecosystems. Recent efforts have revealed the substantial influence that the gut microbiota exert on bee development, food digestion, and homeostasis in general. In this study, deep sequencing was used to characterize prokaryotic viral communities associated with honey bees, which was a blind spot in research up until now. The vast majority of the prokaryotic viral populations are novel at the genus level, and most of the encoded proteins comprise unknown functions. Nevertheless, genomes of bacteriophages were predicted to infect nearly every major bee-gut bacterium, and functional annotation and auxiliary metabolic gene discovery imply the potential to influence microbial metabolism. Furthermore, undiscovered genes involved in the synthesis of secondary metabolic biosynthetic gene clusters reflect a wealth of previously untapped enzymatic resources hidden in the bee bacteriophage community.},
}

@article {pmid31752061,
year = {2019},
author = {Yang, SJ and Kim, HW and Choi, SG and Chung, S and Oh, SJ and Borkar, S and Kim, HJ},
title = {Assessment of the Dynamics of Microbial Community Associated with Tetraselmis suecica Culture under Different LED Lights Using Next-Generation Sequencing.},
journal = {Journal of microbiology and biotechnology},
volume = {29},
number = {12},
pages = {1957-1968},
doi = {10.4010/jmb.1910.10046},
pmid = {31752061},
issn = {1738-8872},
mesh = {Aquaculture ; Bacteria/classification/genetics ; Chlorophyta/genetics/*growth & development/*microbiology/*radiation effects ; Color ; *High-Throughput Nucleotide Sequencing ; *Light ; Metagenomics ; Microbiota/genetics/*physiology ; Oxygen/metabolism ; Photosynthesis ; },
abstract = {Tetraselmis is a green algal genus, some of whose species are important in aquaculture as well as biotechnology. In algal culture, fluorescent lamps, traditional light source for culturing algae, are now being replaced by a cost-effective light-emitting diodes (LEDs). In this study, we investigated the effect of LED light of different wavelengths (white, red, yellow, and blue) on the growth of Tetraselmis suecica and its associated microbial community structures using the next-generation sequencing (NGS). The fastest growth rate of T. suecica was shown in the red light, whereas the slowest was in yellow. The highest OTUs (3426) were identified on day 0, whereas the lowest ones (308) were found on day 15 under red light. The top 100 OTUs associated with day 0 and day 5 cultures of T. suecica under the red and yellow LED were compared. Only 26 OTUs were commonly identified among four samples. The highest numbers of unique OTUs were identified at day 0, indicating the high degree of initial microbial diversity of the T. suecica inoculum. The red light-unique OTUs occupied 34.98%, whereas the yellow-specific OTUs accounted for only 2.2%. This result suggested a higher degree of interaction in T. suecica culture under the red light, where stronger photosynthesis occurs. Apparently, the microbial community associated with T. suecica related to the oxygen produced by algal photosynthesis. This result may expand our knowledge about the algaebacteria consortia, which would be useful for various biotechnological applications including wastewater treatment, bioremediation, and sustainable aquaculture.},
}

Aquaculture
Bacteria/classification/genetics
Chlorophyta/genetics/*growth & development/*microbiology/*radiation effects
Color
*High-Throughput Nucleotide Sequencing
*Light
Metagenomics
Microbiota/genetics/*physiology
Oxygen/metabolism
Photosynthesis

@article {pmid31368841,
year = {2019},
author = {Katsila, T and Balasopoulou, A and Tsagaraki, I and Patrinos, GP},
title = {Pharmacomicrobiomics informs clinical pharmacogenomics.},
journal = {Pharmacogenomics},
volume = {20},
number = {10},
pages = {731-739},
doi = {10.2217/pgs-2019-0027},
pmid = {31368841},
issn = {1744-8042},
mesh = {Databases, Factual ; Drug-Related Side Effects and Adverse Reactions/*genetics ; Host Microbial Interactions/*genetics ; Humans ; Microbiota/*physiology ; Pharmaceutical Preparations/administration & dosage ; Pharmacogenetics/methods ; },
abstract = {Aim: Microbiota-host-xenobiotics interactions in humans become of prime interest when clinical pharmacogenomics is to be implemented. Despite the advent of technology, information still needs to be translated into knowledge for optimum patient stratification and disease management. Material & methods: Herein, we mined metagenomic, pharmacometagenomic and pharmacomicrobiomic datasets to map microbiota-host-drugs networks. Results: Datasets were multifaceted and voluminous. Interoperability, data sparsity and scarcity remain a challenge. Mapping microbiota-host-drugs networks allowed the prediction of drug response/toxicity and modulation of the microbiota-host-drugs interplay. Conclusion: Our approach triangulated microbiota, host and drug networks revealing the need for contextual data and open science via microattribution to accelerate knowledge growth. Our findings may serve as a data storehouse for a user-friendly query system, coupled with databanks and databases.},
}

Databases, Factual
Drug-Related Side Effects and Adverse Reactions/*genetics
Host Microbial Interactions/*genetics
Humans
Microbiota/*physiology
Pharmaceutical Preparations/administration & dosage
Pharmacogenetics/methods

@article {pmid31971995,
year = {2020},
author = {Ben Maamar, S and Glawe, AJ and Brown, TK and Hellgeth, N and Hu, J and Wang, JP and Huttenhower, C and Hartmann, EM},
title = {Mobilizable antibiotic resistance genes are present in dust microbial communities.},
journal = {PLoS pathogens},
volume = {16},
number = {1},
pages = {e1008211},
pmid = {31971995},
issn = {1553-7374},
mesh = {*Air Pollution, Indoor ; Drug Resistance, Microbial/*genetics ; *Dust ; Environmental Microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Metagenomics ; Microbiota/*genetics ; },
abstract = {The decades-long global trend of urbanization has led to a population that spends increasing amounts of time indoors. Exposure to microbes in buildings, and specifically in dust, is thus also increasing, and has been linked to various health outcomes and to antibiotic resistance genes (ARGs). These are most efficiently screened using DNA sequencing, but this method does not determine which microbes are viable, nor does it reveal whether their ARGs can actually disseminate to other microbes. We have thus performed the first study to: 1) examine the potential for ARG dissemination in indoor dust microbial communities, and 2) validate the presence of detected mobile ARGs in viable dust bacteria. Specifically, we integrated 166 dust metagenomes from 43 different buildings. Sequences were assembled, annotated, and screened for potential integrons, transposons, plasmids, and associated ARGs. The same dust samples were further investigated using cultivation and isolate genome and plasmid sequencing. Potential ARGs were detected in dust isolate genomes, and we confirmed their placement on mobile genetic elements using long-read sequencing. We found 183 ARGs, of which 52 were potentially mobile (associated with a putative plasmid, transposon or integron). One dust isolate related to Staphylococcus equorum proved to contain a plasmid carrying an ARG that was detected metagenomically and confirmed through whole genome and plasmid sequencing. This study thus highlights the power of combining cultivation with metagenomics to assess the risk of potentially mobile ARGs for public health.},
}

*Air Pollution, Indoor
Drug Resistance, Microbial/*genetics
*Dust
Environmental Microbiology
Gene Transfer, Horizontal
*Genes, Bacterial
Genome, Bacterial
Metagenomics
Microbiota/*genetics

@article {pmid31261078,
year = {2019},
author = {Valentine, G and Prince, A and Aagaard, KM},
title = {The Neonatal Microbiome and Metagenomics: What Do We Know and What Is the Future?.},
journal = {NeoReviews},
volume = {20},
number = {5},
pages = {e258-e271},
doi = {10.1542/neo.20-5-e258},
pmid = {31261078},
issn = {1526-9906},
mesh = {Female ; Forecasting ; Humans ; Infant Health/*trends ; Infant, Newborn ; Metagenome/*physiology ; Metagenomics/methods/*trends ; Microbiota/*physiology ; Pregnancy ; },
abstract = {The human microbiota includes the trillions of microorganisms living in the human body whereas the human microbiome includes the genes and gene products of this microbiota. Bacteria were historically largely considered to be pathogens that inevitably led to human disease. However, because of advances in both cultivation-based methods and the advent of metagenomics, bacteria are now recognized to be largely beneficial commensal organisms and thus, key to normal and healthy human development. This relatively new area of medical research has elucidated insights into diseases such as inflammatory bowel disease and obesity, as well as metabolic and atopic disorders. However, much remains unknown about the complexity of microbe-microbe and microbe-host interactions. Future efforts aimed at answering key questions pertaining to the early establishment of the microbiome, alongside what defines its dysbiosis, will likely lead to long-term health and mitigation of disease. Here, we review the relevant literature pertaining to modulations in the perinatal and neonatal microbiome, the impact of environmental and maternal factors in shaping the neonatal microbiome, and future questions and directions in the exciting emerging arena of metagenomic medicine.},
}

Female
Forecasting
Humans
Infant Health/*trends
Infant, Newborn
Metagenome/*physiology
Metagenomics/methods/*trends
Microbiota/*physiology
Pregnancy

@article {pmid30784035,
year = {2019},
author = {Leavitt, J and Saleh, N},
title = {The Microbiome and Colorectal Cancer: Current Clinical Trials.},
journal = {Oncology (Williston Park, N.Y.)},
volume = {33},
number = {2},
pages = {78},
pmid = {30784035},
issn = {0890-9091},
mesh = {Bile Acids and Salts/metabolism ; Colorectal Neoplasms/*microbiology/mortality/therapy ; Colorectal Neoplasms, Hereditary Nonpolyposis/microbiology ; Dietary Fiber/administration & dosage ; Fatty Acids, Omega-3/administration & dosage ; Gastrointestinal Microbiome/*physiology ; Humans ; Metagenomics ; Sulfur/metabolism ; },
}

Bile Acids and Salts/metabolism
Colorectal Neoplasms/*microbiology/mortality/therapy
Colorectal Neoplasms, Hereditary Nonpolyposis/microbiology
Dietary Fiber/administration & dosage
Fatty Acids, Omega-3/administration & dosage
Gastrointestinal Microbiome/*physiology
Humans
Metagenomics
Sulfur/metabolism

@article {pmid30478535,
year = {2019},
author = {Cui, J and Cui, H and Yang, M and Du, S and Li, J and Li, Y and Liu, L and Zhang, X and Li, S},
title = {Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade.},
journal = {Protein & cell},
volume = {10},
number = {7},
pages = {496-509},
pmid = {30478535},
issn = {1674-8018},
mesh = {Adult ; Biomarkers/analysis ; Case-Control Studies ; Female ; Gastritis/*microbiology ; Humans ; Male ; *Microbiota ; Middle Aged ; Precancerous Conditions/*microbiology ; Tongue/*microbiology ; },
abstract = {The development of gastritis is associated with an increased risk of gastric cancer. Current invasive gastritis diagnostic methods are not suitable for monitoring progress. In this work based on 78 gastritis patients and 50 healthy individuals, we observed that the variation of tongue-coating microbiota was associated with the occurrence and development of gastritis. Twenty-one microbial species were identified for differentiating tongue-coating microbiomes of gastritis and healthy individuals. Pathways such as microbial metabolism in diverse environments, biosynthesis of antibiotics and bacterial chemotaxis were up-regulated in gastritis patients. The abundance of Campylobacter concisus was found associated with the gastric precancerous cascade. Furthermore, Campylobacter concisus could be detected in tongue coating and gastric fluid in a validation cohort containing 38 gastritis patients. These observations provided biological evidence of tongue diagnosis in traditional Chinese medicine, and indicated that tongue-coating microbiome could be a potential non-invasive biomarker, which might be suitable for long-term monitoring of gastritis.},
}

Adult
Biomarkers/analysis
Case-Control Studies
Female
Gastritis/*microbiology
Humans
Male
*Microbiota
Middle Aged
Precancerous Conditions/*microbiology
Tongue/*microbiology

@article {pmid31779234,
year = {2019},
author = {Leoni, C and Ceci, O and Manzari, C and Fosso, B and Volpicella, M and Ferrari, A and Fiorella, P and Pesole, G and Cicinelli, E and Ceci, LR},
title = {Human Endometrial Microbiota at Term of Normal Pregnancies.},
journal = {Genes},
volume = {10},
number = {12},
pages = {},
pmid = {31779234},
issn = {2073-4425},
mesh = {Adult ; Bacteria/*classification/genetics ; Cesarean Section ; DNA Barcoding, Taxonomic/*methods ; Endometrium/*microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Microbiota ; Phylogeny ; Pilot Projects ; Pregnancy ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Young Adult ; },
abstract = {The endometrium is a challenging site for metagenomic analysis due to difficulties in obtaining uncontaminated samples and the limited abundance of the bacterial population. Indeed, solid correlations between endometrial physio-pathologic conditions and bacteria compositions have not yet been firmly established. Nevertheless, the study of the endometrial microbiota is of great interest due to the close correlations between microbiota profiles, women's health, and successful pregnancies. In this study, we decided to tackle the study of the endometrial microbiota through analysis of bacterial population in women subjected to elective caesarean delivery. As a pilot study, a cohort of 19 Caucasian women at full term of normal pregnancy and with a prospection of elective caesarean delivery was enrolled for endometrium sampling at the time of caesarean section. Sampling was carried out by endometrial biopsy soon after the delivery of the newborn and the discharge of the placenta and fetal membranes from the uterus. Bacterial composition was established by a deep metabarcoding next generation sequencing (NGS) procedure addressing the V5-V6 hypervariable region of the 16S rRNA gene. Amplicon sequences were analysed by bioinformatic procedures for denoising and taxonomic classification. The RDP database was used as 16S rRNA reference collection. Metabarcoding analysis showed the presence of a common bacterial composition, including six genera classifiable within the human microbiota (Cutibacterium, Escherichia, Staphylococcus, Acinetobacter, Streptococcus, Corynebacterium), that could be part of the core endometrial microbiota under the specific conditions examined. These results can provide useful information for future studies on the correlations between bacteria and successful pregnancies.},
}

Adult
Bacteria/*classification/genetics
Cesarean Section
DNA Barcoding, Taxonomic/*methods
Endometrium/*microbiology
Female
High-Throughput Nucleotide Sequencing
Humans
Metagenome
Microbiota
Phylogeny
Pilot Projects
Pregnancy
RNA, Ribosomal, 16S/*genetics
Sequence Analysis, DNA
Young Adult