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dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication


We infer that this, and selection for form II RuBisCOs, are adaptions to high CO2 -concentrations. However, many autotrophs can also grow mixotrophically, a strategy that confers metabolic versatility. The assignment of 156 hydrogenases to 90 different organisms suggests that H2 is an important inter-species energy currency even under gaseous CO2 -saturation. Overall, metabolic analyses at the organism level provided insight into the biochemical cycles that support subsurface life under the extreme condition of CO2 saturation.

Necrotizing enterocolitis (NEC) afflicts approximately 10% of extremely preterm infants with high fatality. Inappropriate bacterial colonization with Enterobacteriaceae is implicated, but no specific pathogen has been identified. coli (UPEC) colonization as a significant risk factor for the development of NEC and subsequent mortality. We describe a large-scale deep shotgun metagenomic sequence analysis of the early intestinal microbiome of 144 preterm and 22 term infants. coli, we identify genes associated with NEC and mortality that indicate colonization by UPEC.

Antimicrobial resistance is a serious threat to global public health, but little is known about the effects of microbial control on the microbiota and its associated resistome. Here we compare the microbiota present on surfaces of clinical settings with other built environments.

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The challenge that arises from independent assembly is that de-replication of the resulting genome set is required (Raveh-Sadka et al., 2015; Probst et al., 2016; Olm et al., 2017). De-replication involves identifying genomes that are the ‘same’ from a larger set, as well as determining the highest quality genome in each replicate set.

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We used a published fecal metagenome data set with known strain heterogeneity to explore the effect of within-population variation on assembly and genome recovery (Sharon et al., 2013). Samples from the single infant were either co-assembled or samples were assembled individually and then de-replicated using dRep. In the case of Staphylococus hominis, co-assembly generated a contaminated bin (that is, many duplicate and triplicate single copy genes; Figure 2a). In contrast, a near-complete, uncontaminated genome was recovered from several individual time-points. Previous work on the same data set (Eren et al., 2015) has shown manual bin curation of the co-assembled bin with anvi’o can increase the S.

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AR genes that are enriched following specific antibiotic treatments are generally unique to the specific treatment and are highly correlated with the abundance of a single species. The most notable exceptions include ticarcillin–clavulanate and ampicillin, both of which enrich for a large number of overlapping AR genes, and are correlated with Klebsiella pneumoniae. We find that all antibiotic treatments are associated with widespread collateral microbiome impact by enrichment of AR genes that have no known activity against the specific antibiotic driver. Metagenome sequencing generates short reads from throughout the genomes of a microbial community.

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Both he and Leonard Garment dismissed Fielding as a possibility, reporting that he had been cleared by Woodward in 1980 when Fielding was applying for an important position in the Reagan administration. Further, while Woodward stressed these precautions in his book, he also admits to having called "Deep Throat" on the telephone at his home. Woodward, in All the President's Men, first mentions Deep Throat on page 71; earlier in the book he reports calling "an old friend and sometimes sources who worked for the federal government and did not like to be called at his office". Later, he describes him as "a source in the Executive Branch who had access to information at CRP as well as at the White House".

Both NOB candidates survived long periods of starvation and the more abundant one formed miniaturized cells and was heat resistant. This detection of novel thermophilic NOB exemplifies our still incomplete knowledge of nitrification, and indicates that nitrite oxidation might be an ancient and wide-spread form of energy conservation.

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DRep: A tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

  • The nitrifying consortia obtained at 70 °C consisted mostly of novel Chloroflexi as revealed by metagenomic sequencing.
  • Nitrifying microorganisms occur across a wide temperature range from 4 to 84 °C and previous studies in geothermal systems revealed their activity under extreme conditions.
  • Combined with deep shotgun sequencing of all stools, we find that multidrug-resistant members of the genera Escherichia, Klebsiella and Enterobacter, genera commonly associated with nosocomial infections, dominate the preterm infant gut microbiota.
  • We find multiple associations between SVs and host disease risk factors, many of which replicate in an independent cohort.

Together with recent analytical advancements, these new methods and technologies have the potential to rapidly advance the field of halophile research. Oxygen minimum zones (OMZs) are marine regions where O2 is undetectable at intermediate depths. Within OMZs, the oxygen-depleted zone (ODZ) induces anaerobic microbial processes that lead to fixed nitrogen loss via denitrification and anammox. Surprisingly, nitrite oxidation is also detected in ODZs, although all known marine nitrite oxidizers (mainly Nitrospina) are aerobes. We used metagenomic binning to construct metagenome-assembled genomes (MAGs) of nitrite oxidizers from OMZs.

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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.

These genomic and protein resources will enable a better understanding of the structure and functions of the rumen microbiota. Advanced treatment facilities for potable water reuse of wastewater are designed to achieve high removal levels of specific pathogens, as well as many other constituents. However, changes to the microbial community throughout treatment, storage, and distribution of this water have not been well characterized. We applied high-throughput amplicon sequencing, read-based, assembly-based, and genome-resolved metagenomics, and flow cytometry to investigate the microbial communities present in a pilot-scale advanced water treatment facility. Advanced treatment of secondary-treated wastewater consisted of ozonation, chloramination, microfiltration, reverse osmosis (RO), advanced oxidation (UV/H2O2), granular activated carbon (GAC) filtration, and chlorination.

A population genomics approach shows widespread geographical distribution of cryptic genomic forms o...

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In 2005, 31 years after Nixon's resignation and 11 years after Nixon's death, a family attorney stated that former Federal Bureau of Investigation (FBI) Associate Director Mark Felt was Deep Throat. By then, Felt was suffering from dementia and had previously denied being Deep Throat, but Woodward and Bernstein confirmed the attorney's claim. Strain heterogeneity reduces genome assembly quality and causes fragmentation in areas of extensive population-level variation. (a) Compared to individual assembly, co-assembly resulted in many duplicate and triplicate single copy genes. (b–d) The Staphylococcus aureus bin obtained from co-assembly is more fragmented than that from an individual assembly.

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Nitrifying microorganisms occur across a wide temperature range from 4 to 84 °C and previous studies in geothermal systems revealed their activity under extreme conditions. Archaea were detected to be responsible for the first step of nitrification, but it is still a challenging issue to clarify the identity of heat-tolerant nitrite oxidizers. In a long-term cultivation approach, we inoculated mineral media containing ammonium and nitrite as substrates with biofilms and sediments of two hot springs in Yellowstone National Park (USA). The nitrifying consortia obtained at 70 °C consisted mostly of novel Chloroflexi as revealed by metagenomic sequencing.

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We also recommend the implementation of an independent nomenclatural system for uncultivated taxa, following the same nomenclature rules as those for cultured Bacteria and Archaea but with its own list of validly published names. If widely adopted, this system will not only facilitate a comprehensive characterization of the ‘uncultivated majority’, but also provide a unified catalogue of validly published names, thereby avoiding synonyms and confusion. We also suggest that a committee of experts, supported by an international microbiological society, should be formed to govern the new classification system. A unifying feature of the bacterial Candidate Phyla Radiation (CPR) is a limited and highly variable repertoire of biosynthetic capabilities. However, the distribution of metabolic traits across the CPR and the evolutionary processes underlying them are incompletely resolved.

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

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.