Tag: MAGs

Structure-guided discovery of anti-CRISPR and anti-phage defense proteins

Identification of putative anti-crispr proteins using structural features To identify Acrs in phage genomes, we began by retrieving ~66.5 million proteins from Integrated Microbial Genomes Virus database (IMG/VR)37. We excluded large proteins because over 90% of known Acrs contain less than 200 amino acids38 (Fig. 1A, Supplementary Data 1). To reduce computational…

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DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea

Description This version is to stay up to date with the improvements and increase in 16S rRNA gene sequences (SSU) added to the GTDB release 214.1.  Please read this post for the stats on the updates. gtdb.ecogenomic.org/stats/r214 . There has been no change to the RDP-RefSeq reference database If anyone…

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Binning the rare biosphere

Hello everyone. I would like to start a discussion here. Recently, I responded to a question on Seqanswers regarding the binning of rare microbes from shotgun metagenomes (www.seqanswers.com/forum/applications-forums/metagenomics/324515-software-recommendation-for-metagenome-assembly-for-low-abundance-bacteria). I suggested an idea for an appropriate pipeline for this task, but unfortunately, it did not gain much attention. Nevertheless, I tried…

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Challenges in Estimating Effective Population Sizes from Metagenome-Assembled Genomes

1Shenzhen Research Institute, The Chinese University of Hong Kong, China 2State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology (CAS), China The final, formatted version of the article will be published soon. Notify me Receive an email when…

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Bioactive glycans in a microbiome-directed food for children with malnutrition

Collection and handling of biospecimens obtained from participants in the randomized controlled clinical study of the efficacy of MDCF-2 The human study entitled ‘Community-based clinical trial with microbiota-directed complementary foods (MDCFs) made of locally available food ingredients for the management of children with primary moderate acute malnutrition (MAM)’ was approved…

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total 30,851 single-cell genomes, 51 metagenomes, and 1,544 metagenome-assembled genomes from the human oral/gut microbiota

README This is the large single amplified genome calatog (bbsag20) corresponding to the publication below: Title: “Single Amplified Genome Catalog Reveals the Dynamics of Mobilome and Resistome in the Human Microbiome” (preprint: 10.1101/2023.12.06.570492) Authors: Tetsuro Kawano-Sugaya, Koji Arikawa, Tatsuya Saeki, Taruho Endoh, Kazuma Kamata, Ayumi Matsuhashi, and Masahito Hosokawa Research…

Continue Reading total 30,851 single-cell genomes, 51 metagenomes, and 1,544 metagenome-assembled genomes from the human oral/gut microbiota

Widespread Bathyarchaeia encode a novel methy

image:  A. The relative abundance of microbial populations based on 16S rRNA gene-tag sequencing analysis before purification by adding antibiotics. B.Growth curves of Ca. B. ligniniphilus in anaerobic medium supplemented with lignin. The error bars were obtained from triplicate Q-PCR reactions. C.The relative abundance of microbial populations based on 16S…

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Carbohydrates and carbohydrate degradation gene abundance and transcription in Atlantic waters of the Arctic

Seawater samples were collected from surface waters (SRF) and the bottom of the surface mixed layer (BML) in the Eastern Fram Strait region to investigate the distribution of carbohydrates and their utilisation by microbial communities. The ten sites were grouped into three categories based on the underlying seafloor topography (above-slope,…

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Resin acids play key roles in shaping microbial communities during degradation of spruce bark

Bark preparation Spruce bark was obtained from the Iggesund pulp and paper mill (Iggesund, Holmen AB, Sweden), from a bark pile resulting from stripping of spruce logs at the mill after harvest, with the average age of trees at harvest being ~70 years. The bark was left to dry at…

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Refinement of the “ Candidatus Accumulibacter” Genus Based on a Metagenomic Analysis of Biological Nutrient Removal (BNR) Pilot-Scale Plants Operated with Reduced Aeration

Abstract Members of the “ Candidatus Accumulibacter” genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 “ Ca . Accumulibacter” species, which have been proposed based on the phylogenetic divergence of the polyphosphate…

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Using metagenome assembly and binning to identify and mitigate contamination in a genome

Hi everyone, This may be a silly question, but I am interested if using metagenome assembly and binning is a valid method of determining if a sample contains a mixture of species. Similarly, can metagenomics be used to identify and remove contamination from a single genome? For some background, I…

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filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts

filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts 0 hi folks, apologies if this has been answered elsewhere. I’m using read mapping to quantitate the abundance of viral metagenome assembled genomes (MAGs) across samples and I’d like to do a bit of data cleaning that’s…

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Minimalist Or Maximalist? The Life Of A Microbe A Mile Underground

Prof. Magdalena Osburn removes a sample during a site visit in August. CREDIT Sanford Underground Research Facility If you added up all the microbes living deep below Earth’s surface, the amount of biomass would outweigh all life within our oceans. But because this abundant life is so difficult to reach,…

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Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel.

Suarez C, Hackl T, Wilen BM, Persson F, Hagelia P, Jetten MSM, Dalcin Martins P FEMS Microbiol. Lett. 370 (-) – [2023-01-17; online 2023-06-09] The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion…

Continue Reading Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel.

Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface

Sampling sites and depths Metagenomes were produced from sediment samples at drilling sites U1545B to U1549B that follow a northwest-to-southeast transect across the northwestern flanking region of Guaymas Basin (Fig. 1A) and include an off-axis hydrothermal system, the Ringvent site (Fig. 1B). The samples were selected to coordinate with depths used for…

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Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster | Microbiome

Diversity of the RCA cluster and genome characteristics The phylogenomic analysis yielded three major clades within the RCA cluster (Fig. 1) Genomes of the three clades were relatively distinct with appr. < 70% average nucleotide identity (ANI), resulting in the proposal of three genera, the known genus Planktomarina, and two new genera without…

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Phylogenetic tree for my bins with abundance, genome size etc

I would like to create a tree for my MAGs/Bins like the image shown below. Can anyone please share me the steps/scripts in detail? When I used, gtdbtk de_novo_wf to analyze a set of bin files with -skip_gtdb_refs. I always ends up with the following error. [2023-11-20 12:55:35] INFO: Read…

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Data_Sheet_3_First shotgun metagenomics study of Juan de Fuca deep-sea sediments reveals distinct microbial communities above, within, between, and below sulfate methane transition zones.xlsx

The marine deep subsurface is home to a vast microbial ecosystem, affecting biogeochemical cycles on a global scale. One of the better-studied deep biospheres is the Juan de Fuca (JdF) Ridge, where hydrothermal fluid introduces oxidants into the sediment from below, resulting in two sulfate methane transition zones (SMTZs). In…

Continue Reading Data_Sheet_3_First shotgun metagenomics study of Juan de Fuca deep-sea sediments reveals distinct microbial communities above, within, between, and below sulfate methane transition zones.xlsx

Online metagenomics training (free) in April

Free Cloud-SPAN course on METAGENOMICS 11-21 April 2023  Join our experts for this free online module! We welcome environmental scientists who would like to use high performance computing for metagenomics analysis, or anyone with an interest in metagenomics to register. No previous experience of the command line or HPC is…

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Forecasting the dynamics of a complex microbial community using integrated meta-omics

Characterization of the microbial community From the experimental period between 21 March 2011 and 3 May 2012 (ref. 27), we previously obtained and analysed 51 weekly samples, to which we added 21 samples collected in the month of June during the years 2012–2016. The 72 samples were submitted to the…

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A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources

40,039 MAGs reconstructed from large-scale genome-resolved metagenomics To reconstruct previously unexplored bacterial and archaeal genomes, we performed a large-scale single-sample metagenomic assembly on 3304 soil metagenomes across the globe (Fig. 1a), including 363 metagenomes from the in-house dataset and 2941 from publicly available metagenomes. The soil samples were mainly collected from…

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Metagenome-assembled genomes from High Arctic glaciers highlight the vulnerability of glacier-associated microbiota and their activities to habitat loss

doi: 10.1099/mgen.0.001131. Affiliations Expand Affiliations 1 Department of Life Sciences (DLS), Aberystwyth University, Wales, UK. 2 Interdisciplinary Centre for Environmental Microbiology (iCEM), Aberystwyth University, Wales, UK. 3 Department of Geography and Earth Sciences (DGES), Aberystwyth University, Wales, UK. 4 Present address: Department of Pathobiology and Population Sciences, The Royal Veterinary…

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Textbook knowledge turned on its head: 3-in-1 microorganism discovered

Phylogenomic reconstruction and metabolic potential of 19 Acidobacteriota metagenome assembled genomes (MAGs) recovered in this study. MAGs from this study (bold) that contained dsrAB are highlighted in red. The class is indicated at the left of the phylogenetic tree and family affiliation on the right (according to GTDB taxonomy99). Abbreviations…

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Revio metagenomics + Kinnex 16S data release demonstrate futuristic microbiome capabilities

Microbiology forms the bedrock of modern genetics and biotechnology. Whether its basic science, alternative energy development, drug discovery, or human health – our planet’s smallest organisms play a critical role in the bigger picture. Even so, most microbial life remains unknown to science. And that’s why cutting-edge microbial ecology and…

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Fruit- and Vegetable-Derived Microbes Contribute to Gut Microbiome Diversity, Study Shows

Diversity of the gut microbiota is crucial for human health. A new study provides the first evidence of the interconnection between the plant and the gut microbiome. The connection is established mainly by three bacterial orders (Enterobacterales, Burkholderiales, and Lactobacillales), which, interestingly, harbor members of both plant and human probiotics….

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Recovery of 52 bacterial genomes from the fecal microbiome of the domestic cat (Felis catus) using Hi-C proximity ligation and shotgun metagenomics.

Abstract We used Hi-C proximity ligation with shotgun sequencing to retrieve metagenome-assembled genomes (MAGs) from the fecal microbiomes of two domestic cats (Felis catus). The genomes were assessed for completeness and contamination, classified taxonomically, and annotated for putative antimicrobial resistance (AMR) genes. Many UC-authored scholarly publications are freely available on…

Continue Reading Recovery of 52 bacterial genomes from the fecal microbiome of the domestic cat (Felis catus) using Hi-C proximity ligation and shotgun metagenomics.

Metagenome-assembled genomes reveal carbohydrate degradation and element metabolism of microorganisms inhabiting Tengchong hot springs, China

. 2023 Sep 15;238(Pt 1):117144. doi: 10.1016/j.envres.2023.117144. Online ahead of print. Affiliations Expand Affiliations 1 State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China. 2 State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College…

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Analysis finds diversity on the smallest scales in sulfur-cycling salt marsh microbes

Cowlicks in salt marsh grass (Sporobolus pumilus) in the Plum Island Ecosystem Long-Term Ecological Research reserve, which is administrated by the MBL Ecosystems Center. Credit: David S. Johnson. Credit: David S. Johnson & Marine Biological Laboratory At the surface, salt marshes and their windswept grasses can look deceptively simple. But…

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Metagenome Assembled Genomes (MAG) Facilitate a Better Understanding of Microbially-mediated Heavy Metal Resistance in Soils from a Former Nuclear Materials Production Facility

Abstract Shotgun metagenomes is a repository of all the genes present in an environmental sample. With recent advancements in bioinformatic techniques, it is now possible to in-silico retrieve sequences that belong to specific taxa, followed by assembly and annotation and the obtained sequences are called as metagenome-assembled genome (MAG), which…

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Study shows the microbiome of fruit and vegetables positively influences diversity in the gut

Overview of the bioinformatic workflow for the recovery of metagenome-assembled genomes (MAGs) from fruits and vegetables and the detection of their presence in the gut. Credit: Gut Microbes (2023). DOI: 10.1080/19490976.2023.2258565 Bacterial diversity in the gut plays an important role in human health. The crucial question, however, is where are…

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transforming medicine with microbiome magic

In this interview, Anne Neville, Director at Microbiotica, elaborates on the significance of the Microbiotica Culture Collection (MCC) and Microbiotica Reference Genome Database (MRGD), which are fundamental to the development of live biotherapeutic medicines. Live Bacterial Products (LBPs) will provide patients with a desirable, credible, safe and effective treatment option….

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What are unbinned contigs ?

What are unbinned contigs ? 1 Hello community, by taking a look into the number of binned contigs from a binning refinement procedure I notice that the number of contigs employed to make bins or MAGs are less than half of the number of contigs produced by the assembly procedure….

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Webinar: Metagenome quantitative SIP at JGI

 The DOE Joint Genome Institute offers metagenome quantitative stable isotope probing (Metagenome – qSIP) capabilities to investigate metabolic activity of metagenome-assembled genomes (MAGs). The JGI Metagenome – qSIP workflow begins with users carrying out isotope enrichment culturing and DNA extractions which are sent to the JGI for sample processing….

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Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space

Viromics datasets represent the sequence space of protected extracellular DNA (peDNA) The majority of samples prepared for “viromics” include GTAs and EVs, in addition to virus particles. All three entities are small protein- and/or lipid-containing particles that can enclose cellular DNA [3] or were found to bind cellular DNA on…

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Metagenome sequencing and recovery of 444 metagenome-assembled genomes from the biofloc aquaculture system

Uncultured microorganisms constitute a significant proportion of microbial populations in an ecosystem and play a vital role in its functioning1. The challenges associated with cultivating these microbes have constrained access to the vast phylogenetic and functional diversity they possess. However, recent advancements in metagenomics have opened a new window to…

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Northeastern Indian Ocean metagenome dataset

Data for contigs, MAGs and other files generated using the Northeastern Indian Ocean microbial dataset. Dataset includes: EIO-MAG.tar.gz 675 non-redundant prokaryotic genomes with ≥ 50% completeness and ≤ 5% contamination. EIO-Contigs.tar.gz: the contigs generated from 25 metagenome. Table.S1:Sampling information and environment factors. Table.S2:The ASVs-table and MAG information. Funding This work…

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Online metagenomics training (free) in November 2023

Free Cloud-SPAN course on METAGENOMICS Monday 6th to Friday 24th November 2023. Join our experts for this free online workshop! We welcome environmental scientists who would like to use high performance computing for metagenomics analysis, or anyone with an interest in metagenomics to register. No previous experience of the command…

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Widespread occurrence of chitinase-encoding genes suggests the Endozoicomonadaceae family as a key player in chitin processing in the marine benthos

Genes coding for endo-chitinases (EC 3.2.1.14), the enzymes that cleave chitin polymers into oligomers [16], were found on 32 of 42 Endozoicomonadaceae genomes (Fig. 1 and Table S1), including representatives of all formally described genera and all Candidatus Gorgonimonas MAGs. Several genomes harbored more than one endo-chitinase encoding gene, resulting in…

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Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease | Genome Biology

Zhang L, Wang F, Wang L, Wang W, Liu B, Liu J, Chen M, He Q, Liao Y, Yu X, et al. Prevalence of chronic kidney disease in China: a cross-sectional survey. Lancet. 2012;379:815–22. Article  PubMed  Google Scholar  Collaboration GBDCKD. Global, regional, and national burden of chronic kidney disease, 1990–2017:…

Continue Reading Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease | Genome Biology

On the relationship between protist metabarcoding and protist metagenome-assembled genomes

Abstract The two most commonly used approaches to study the composition of environmental protist communities are marker gene metabarcoding and whole genome analysis through metagenomics. Raw metabarcoding data are usually processed into Operational Taxonomic Units (OTUs) or amplicon sequence variants (ASVs) through clustering or denoising approaches, respectively. Analogous approaches have…

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MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data

Real metaHi-C datasets In this study, we leveraged several publicly available metagenomic Hi-C datasets, consisting of two short-read metaHi-C datasets and two long-read metaHi-C datasets. The specific sizes of raw datasets were shown in Supplementary Table 6. Two short-read metaHi-C datasets were generated from different microbial ecosystems, including human gut (BioProject:…

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“State-of-the-art Approaches for Sequencing, Assembling and Annotating ” by Henry H. Say

Abstract Naphthenic acids (NAs) are the main toxic component of oil refinery wastewater and require special processes to be removed. Harnessing bacterial biodegradation for NA removal has the potential to be effective, yet NA-degrading bacteria and pathways are poorly understood and uncharacterized. To improve our understanding of NA degradation, I…

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Quality MAGnified | Nature Reviews Microbiology

Decreasing sequencing costs and steady improvements to contig assembly and binning algorithms have led to an explosion of metagenome-assembled genomes (MAGs) derived from microbial communities. These MAGs provide insights into the metabolic potential of community members, which is particularly important for the uncultivated microorganisms whose ecological activities might otherwise remain…

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Deepurify: a multi-modal deep language model to remove contamination from metagenome-assembled genomes

Abstract Metagenome-assembled genomes (MAGs) offer valuable insights into the exploration of microbial dark matter using metagenomic sequencing data. However, there is a growing concern that contamination in MAGs may significantly impact the downstream analysis results. Existing MAG decontamination methods heavily rely on marker genes but do not fully leverage genomic…

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EMBL-EBI Training course | Metagenomics bioinformatics at MGnify

Learn about the tools, processes, and analysis approaches used by MGnify in the field of genome-resolved metagenomics. This course will cover the use of publicly available resources to manage, share, analyse, and interpret metagenomics data, focussing primarily on the assembly-based approaches used in MGnify analysis. The delivered content will involve…

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A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins

Construction of integrated PCEG and PCEP To the best of our knowledge, the present study is the first to develop a comprehensive catalog of plastic-contaminated soils using an integrated bioinformatic workflow. Five datasets were used to produce 53,300,583 unique genes and proteins. Quality control of reads, trimming, assembly, and binning…

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Microbiome and metabolome in home-made fermented soybean foods of India revealed by metagenome-assembled genomes and metabolomics

Grep-chhurpi, peha, peron namsing and peruñyaan are lesser-known home-made fermented soybean foods prepared by the native people of Arunachal Pradesh in India. Present work aims to study the microbiome, their functional annotations, metabolites and recovery of metagenome-assembled genomes (MAGs) in these four fermented soybean foods. Metagenomes revealed the dominance of…

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The leaderless communication peptide (LCP) class of quorum-sensing peptides is broadly distributed among Firmicutes

Leaderless communication peptide (LCP) system is broadly distributed To assess the distribution of SIP-like LCP-based qs systems across bacteria, we employed a large-scale search strategy that includes: (i) search for RopB homologs across a dataset of 129,001 bacterial genomes and 9,421 reference metagenomics-assembled genomes (MAGs), (ii) probing the genomic vicinity…

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Data from: Metagenomes and Metagenome-Assembled Genomes from Ex Vivo Fecal Incubations of Six Unique Donors

This is a dataset consisting of donor-specific collections of 78 metagenomes (13 / donor) and 143 metagenome-assembled genomes (MAGs) representing the gut microbiomes of six healthy adult human donors. Raw sequencing data and MAG sequence data will be available in NCBI under BioProject accession PRJNA961974 (www.ncbi.nlm.nih.gov/bioproject/PRJNA961974). Spreadsheets attached to this…

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Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning [PeerJ]

Introduction The rapid proliferation of high-throughput sequencing in metagenomics, combined with the advancement of scalable computational tools, has allowed scientists to digitally isolate tens of thousands of microbial genomes from large collections of metagenomic datasets (Nayfach et al., 2021). Although these genomes are only the tip of the iceberg of…

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Clinical Microbiomics debuts “revolutionary” human microbiome profiling tool

21 Sep 2023 — Denmark-based Clinical Microbiomics has developed the Human Microbiome Profiler 2.0 called Champ, which is set to accelerate microbiome research by maximizing insights from data and minimizing the risk of false discoveries. Demonstrating high sensitivity and accuracy in microbiome profiling, Champ leverages Clinical Microbiomics’…

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Fast and robust metagenomic sequence comparison through sparse chaining with skani

Sequence identity estimation Formally, let G be a string of nucleotides and \({G}^{{\prime} }\) be a mutated version of G where every letter is independently changed to a different letter with probability θ. We will define the true ANI to be equal to 1 − θ under our model. Under the usual…

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A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil

Field sample collection Topsoil samples (0–15 cm, roughly 0.5 m3) from replicate field plots were collected from the Hopland Research and Extension Center (HREC) in Northern California, which is unceded land of the Shóqowa and Hopland People, on August 28th, 2018 after experiencing mean annual precipitation during the rainy season, see our…

Continue Reading A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil

Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut

A taurine-respiring bacterium isolated from the murine gut represents a new genus of the family Desulfovibrionaceae Strain LT0009 was enriched from mouse cecum and colon using an anoxic, non-reducing, modified Desulfovibrio medium with L-lactate and pyruvate as electron donors (and carbon source) and taurine as the sulfite donor for sulfite…

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A whole new order of bacteria could hold the key to improving biogas production

(A) Dendrogram of all the HQ and GQ MAGs from MICRO4BIOGAS (n=1053), computed with UBCG and visualized with iTOL. The legend shows a classification by different colors corresponding to different phyla, according to the annotation obtained with GTDB-tk (v 2.1.1), and a highlight on MBA03 (within Bacillota). (B) Tree with…

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Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety

Study design We set up a prospective, double-blinded, randomised, placebo-controlled intervention study that was performed in our academic hospital, the Amsterdam University Medical Centres location AMC in the Netherlands. After passing screening, 24 subjects with MetSyn were randomised to receive a sterile FFT from a lean healthy donor or a…

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Metagenomics and metagenome-assembled genomes mining of health benefits in jalebi batter, a naturally fermented cereal-based food of India

Jalebi is one of the oldest Indian traditional fermented wheat-based confectioneries. Since jalebi is prepared by natural fermentation, diverse microbial community is expected to play bio-functional activities. Due to limited studies, information on microbial community structure in jalebi is unknown. Hence, the present study is aimed to profile the microbial…

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Cloud-SPAN course: Metagenomics | Software Sustainability Institute

Cloud-SPAN will host a free course on metagenomics from Monday 6, until Friday 24 November 2023. The course is aimed at environmental scientists who would like to use high performance computing for metagenomics analysis or anyone interested in metagenomics. No previous experience of the command line or HPC is required. The deadline to…

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Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions

Reactor performance revealed temporal changes in propionate degradation rate The four propionate- and acetate-fed reactors used in the study produced biogas with an average methane content of 62–70% (Table S2). The pH was 8.1–8.3, resulting in an ammonia-nitrogen level of 0.7–0.9 g NH3 L-1. This free ammonia level is well above…

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Partition reads in BAM file by MAG

Partition reads in BAM file by MAG 0 Hi all, I have bins representing MAGs. I am now interested in partitioning the reads in my BAM files by MAG. The way I believe this should work is to try and map every read onto the MAG, asses whether it maps…

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Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation

Location and sample collection Samples were taken from 10 composting piles (between May and August 2020) at a food waste (FW) composting facility (Zhejiang, China; 30°52′51.50″N; 119°46′12.87″E). A consistent pre-treatment method was used for each pile. Specifically, about 8 tons of FW was collected every 3 days and subsequently crushed into…

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Gone with a trace: cataloguing the disappearing gut microbes

This month’s Genome Watch highlights the use of high-depth genome-centric approaches to further our understanding of the human gut microbiome within the context of industrialized and non-industrialized lifestyles. Poor gut health and the rise of non-communicable chronic diseases (NCCDs) such as cardiovascular disease and diabetes have been increasingly linked to…

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Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater

Lulu Island waste resource recovery ecosystem The Lulu Island WWTP operated by Metro Vancouver in Richmond, British Columbia, Canada (Longitude: −123.14498° or 123° 8’ 42” W, Latitude: 49.11491° or 49° 6’ 54” N) provides primary and secondary treatment of >30 billion liters of mixed-sourced wastewater from ~200,000 residents each year….

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Genome coverage of MAGs while submitting to NCBI

Genome coverage of MAGs while submitting to NCBI 1 Hello everyone. I am trying to submit my metagenome assembled genomes to NCBI through its “genome submission portal”. It asks me about the genome coverage of my genome. What exactly should I specify, considering I submitting MAGs? I have no expected…

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Metagenomic and culture-dependent approaches unveil active microbial community and novel functional genes involved in arsenic mobilization and detoxification in groundwater | BMC Microbiology

Hydrogeochemical properties of the arsenic-contaminated groundwater The hydrological and geochemical properties of the analyzed GW samples are summarized in Table 2. Temperature, pH, and dissolved oxygen (DO) levels were within acceptable limits for drinking water in all samples. The average temperature and pH of the As-contaminated GW samples were 27.33°C…

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Science: Metagenome sequencing reveals pathogen-mediated plant endophytes

Yi Gene|Science: Metagenome sequencing reveals pathogenic bacteria-mediated activation of plant endophyte disease-suppressive function Using metagenomics techniques of plant endophytes, researchers such as Carrión of the Netherlands Institute for Ecology have shown that certain “resident” bacteria can protect plant roots from fungal infection. It is revealed that microorganisms living inside plant…

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Automappa: An interactive interface for metagenome-derived genome bins

Abstract Background: Studies attempting to observe microbes commonly considered uncultivable under standard laboratory conditions are turning to so-called “deep” environmental sequencing approaches whereby they may access these unculturable organisms’ genomes via in silico approaches. A typical workflow involves metagenome assembly, annotation, and binning for reconstruction of each respective organism’s genome…

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Microbiome-directed foods boost child nutrition

In a recent study posted to the medRxiv* preprint server, researchers reconstructed gut bacterial genomes. The study identified metabolic pathways that are differentially expressed in response to a microbiota-directed complementary food prototype (MDCF-2) in metagenome-assembled genomes (MAGs) related to changes in weight-for-length Z scores (WLZ). They also evaluated the impact…

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BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

Background: Exploring metagenomic contigs and “binning” them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human…

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Metagenomics Untangles Metabolic Adaptations Of Antarctic Endolithic Bacteria At The Fringe Of Habitability

Maximum likelihood phylogenetic tree of [NiFe]-hydrogenase gene sequences obtained from our MAGs (n = 2433), with reference sequences obtained from the HydB and previous phylogenetic analysis. Branches and reference gene labels are colored according to the group of [NiFe]-hydrogenase. Bootstrap values >90% are depicted as filled circles on branches, with…

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Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil

Nitrososphaeria AOA dominate archaeal and nitrifier assemblage throughout the year Nitrososphaeria AOA represented 79.4–100%, 75.4–98.0%, and 73.4–98.6% of total archaea and 2.8–7.6%, 1.0–1.8%, and 1.2–2.3% of total microbial communities in 16S rRNA gene amplicon, metagenome-recovered 16S rRNA genes, and prokaryotic rpoB-normalized amoA gene reads, respectively, throughout the year (Fig. 1A–C). Non-ammonia-oxidizing…

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Metagenomes Assembles Genomes from cultivated freshwater bacterial communities

This dataset represents 122 Metagenomes-Assembled Genomes (MAGs) that were reconstructed from 20 individual microcosms in the context of understanding microbial community assembly processes. The cultivation media consisted in Artificial Lake Water (ALW) enriched with glucose and cellobiose (See details in Le Moigne et al., 2023, Ecology). The microcosms (200 mL)…

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Characterization of the pig lower respiratory tract antibiotic resistome

Composition and distribution of ARGs in the pig lower respiratory tract microbiome Using 745 metagenome data of the lower respiratory tract microbiome from 675 experimental pigs across five populations, we constructed a swine respiratory microbial gene catalog containing 10,337,194 non-redundant genes. Of these, 1228 open reading frames (ORFs) were identified…

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Comprehensive catalogs for microbial genes and metagenome-assembled genomes of the swine lower respiratory tract microbiome identify the relationship of microbial species with lung lesions

Abstract Understanding the community structure and functional capacity of the lower respiratory tract microbiome is crucial for elucidating its roles in respiratory tract diseases. However, there are few studies about it owing to the difficulty in obtaining microbial samples from the lower respiratory tract. Here we collected 745 microbial samples…

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SeqCode Provides Path to Name Uncultivated Prokaryotes

The name elephant. Investigators from different disciplines examine different portions of a microorganism and develop their own opinions about its nature. Precise scientific names enable the unification of information from disparate disciplines and laboratories to create a single, multifaceted vision. Source: William Whitman and Brian Hedlund Most prokaryotes have never…

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Would you recommend me a binning tool ?

Would you recommend me a binning tool ? 1 Hello! , on the last months I have been producing some metagenome assembled genomes from different datasets, for this purpose I’m currently using metabat2, vamb and CONCOCT. The problem is that CONCOCT takes too much time to run and its a…

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Phylogenomic trees of MAGs isolated from lichen metagenomes

Supplementary files associated with Tagirdzhanova et al. 2023. A global survey of lichen symbionts from metagenomes Maximum likelihood phylogenetic trees of the MAGs isolated from lichen metagenomes.  Includes three files:  1. bacterial.treefile  This tree was calculated using IQ-TREE and are based on alignments of marker genes (for prokaryotes: 120 marker…

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Genetic strategies for sex-biased persistence of gut microbes across human life

Strain dynamics of the gut-associated microbiota within the first 24 months of life Shotgun metagenomics sequencing approaches were applied to the microbiomes of 11 healthy, vaginally delivered, full-term (>37 weeks of gestation) newborns, which were longitudinally sampled at 1-, 6-, 12-, and 24-months following birth (Figs. S1, S2, Supplementary Data 1). Consistent with…

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Analyzing methylation in a metagenome

Analyzing methylation in a metagenome 0 Hello all, I am interested in understanding the DNA methylation present in a bacterial metagenome. I have sequenced the metagenome using nanopore, and used their basecaller dorado to obtain bam files annotated with the DNA modifications I am interested in. I am looking for…

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CIMB | Free Full-Text | A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseumonadota

1. Introduction One characteristic of many geothermal fields is the presence of steam vents, i.e., fumaroles, that consist of permanent emissions of steam and gases from the subsoil due to magmatic activity or groundwater geothermal heating [1]. Consequently, the steam has temperatures above 70 °C, wet conditions, and a concentration…

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Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs

Abstract We introduce a novel metagenomics assembler for high-accuracy long reads. Our approach, implemented as metaMDBG, combines highly efficient de Bruijn graph assembly in minimizer space, with both a multi-k’ approach for dealing with variations in genome coverage depth and an abundance-based filtering strategy for simplifying strain complexity. The resulting…

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Global within-species phylogenetics of sewage microbes suggest that local adaptation shapes geographical bacterial clustering

Predominant bacteria in sewage do likely not originate from the human gut To identify bacterial genomes from sewage across the world, we used a combination of two different metagenomics genome binners (VAMB24 and MetaBAT225). From 757 samples across 101 different countries (Fig. 1a and Supplementary Fig. 1), we were able to create…

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How to add a refseq() slot to a MAG based phyloseq object ?

How to add a refseq() slot to a MAG based phyloseq object ? 0 Hello, I was asked to build a phyloseq object from some metagenome assembled genomes that I built. By far I have created a tax_table() slot from the classification of the MAGs using GTDB-Tk, a out_table() that…

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MT-MAG: Accurate and interpretable machine learning for complete or partial taxonomic assignments of metagenome-assembled genomes

Abstract We propose MT-MAG, a novel machine learning-based software tool for the complete or partial hierarchically-structured taxonomic classification of metagenome-assembled genomes (MAGs). MT-MAG is alignment-free, with k-mer frequencies being the only feature used to distinguish a DNA sequence from another (herein k = 7). MT-MAG is capable of classifying large…

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Depth file for Metabat2

Depth file for Metabat2 1 Hello, I am currently binning using Metabat2 and I have 5 samples that I have decided to assemble individually as opposed to a coassembly. However, for each assembly I did create sorted bam files for all 5 of my samples reads, since they are from…

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[Detailed Question] How to Normalize of Metagenomics Gene Abundances (with HMMs models)

Hi everyone, Me and my colleagues have been thinking about normalization for quite some time, and we have a hard time finding a consensus both within us, and within the literature, for this reason, this is going to be a long and detailed post. Talking with other researchers we feel…

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Growth rate is a dominant factor predicting the rhizosphere effect

Rhizosphere bacteria have shorter predicted doubling times than soil bacteria To investigate whether growth rate potential predictions correlate with rhizosphere enrichment, we re-analyzed previously published metacommunities. These included rhizospheres and associated bulk soil microbiomes from 18 different plant genotypes and conditions such as: Arabidopsis thaliana ecotypes and sister species [9],…

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Terabase-Scale Coassembly of a Tropical Soil Microbiome

Petabases of environmental metagenomic data are publicly available, presenting an opportunity to characterize complex environments and discover novel lineages of life. Metagenome coassembly, in which many metagenomic samples from an environment are simultaneously analyzed to infer the underlying genomes’ sequences, is an essential tool for achieving this goal. We applied…

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Metagenomics analysis reveals differences in rumen microbiota in cows with low and high milk protein percentage

Variation exists in milk protein concentration of dairy cows of the same breed that are fed and managed in the same environment, and little information was available on this variation which might be attributed to differences in rumen microbial composition as well as their fermentation metabolites. This study is aimed…

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Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems

Geochemical evolution of groundwater in the Canadian Prairie The mean residence time of water in an aquifer is a very important factor influencing its geochemical composition (or facies) (Fig. 2a). Mean residence time, or groundwater age, is determined using radioisotopes such as tritium and 14C and refers to the travel time…

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Charms to Soothe the Savage Microbiome

By Kathy Liszewski When we say it’s the little things that count, we seldom consider whether those things could include microbes. We’re too aware of microbes like flesh-eating bacteria, respiratory viruses, and other pathogens. But not all microbes are sources of invariable dread. Many microbes are innocuous or even beneficial….

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Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants

Awasthi MK, Singh E, Binod P, Sindhu R, Sarsaiya S, Kumar A, et al. Biotechnological strategies for bio-transforming biosolid into resources toward circular bio-economy: a review. Renew Sustain Energy Rev. 2022;156:111987. Article  CAS  Google Scholar  Diamantis V, Eftaxias A, Stamatelatou K, Noutsopoulos C, Vlachokostas C, Aivasidis A. Bioenergy in the…

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Persistence of Antibiotic Resistance from Animal Agricultural Effluents to Surface Water Revealed by Genome-Centric Metagenomics

Author links open overlay panelJin Ju Kim a 1, Hoon Je Seong a b 1, Timothy A. Johnson c, Chang-Jun Cha a, Woo Jun Sul a, Jong-Chan Chae d Show more doi.org/10.1016/j.jhazmat.2023.131761Get rights and content ABSTRACT Concerns about antibiotic resistance genes (ARGs) released from wastewaters of livestock or fish farming…

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Characterization of metagenome-assembled genomes from the International Space Station | Microbiome

Metagenome-assembled bacterial genomes Out of the 42 ISS metagenomes submitted at NCBI, only PMA-treated metagenomes (n = 21) representing the viable/intact cells were used for generating bacterial MAGs. Characteristics of MAGs (n = 46) such as genome size (2.6 to 6.6 Mb), completeness, contamination percentage, the average mean coverage, number…

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Not annotated metagenome-assembled genomes recovered from rumen samples from cows

  Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the genera Entodinium has been consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that species such as Entodinium caudatum exert, their greater…

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A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters

Revsbech, N. P. et al. Determination of ultra-low oxygen concentrations in oxygen minimum zones by the STOX sensor. Limnol. Oceanogr.: Methods. 7, 371-381. (2009). Wright, J. J., Konwar, K. M. & Hallam, S. J. Microbial ecology of expanding oxygen minimum zones. Nat. Rev. Microbiol. 10, 381–394 (2012). Article  CAS  PubMed …

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Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach

The infant and maternal gut microbiota are defined by different Bifidobacterium species The samples analysed in this study were collected during the MicrobeMom study (ISRCTN5302301420,21), these included samples from the maternal stool, vagina, oral cavity, and breast milk in addition to infant stool (Table 1; Fig. 1a). From the 160 participants recruited,…

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Gut microbiome signatures of extreme environment adaption in Tibetan pig

1050 SGBs clustered from 8210 high-medium quality metagenome-assembled genomes (MAGs) Over 779 Gb metagenomic sequence data was generated by Illumina HiSeq × Ten platform from 65 TPs samples (Supplementary Table 1). We integrated the above sequencing raw reads with a published metagenomic sequence dataset of 287 captive pigs from Denmark, France…

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Metagenomics reveals the habitat specificity of biosynthetic potential of secondary metabolites in global food fermentations

Background: Fermented foods are considered to be beneficial for human health. Secondary metabolites determined by biosynthetic gene clusters (BGCs) are precious bioactive compounds with various biological activities. However, the diversity and distribution of the biosynthetic potential of secondary metabolites in global food fermentations remain largely unknown. In this study, we…

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Table1_A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate.XLSX

Fermentative microbial communities have the potential to serve as biocatalysts for the conversion of low-value dairy coproducts into renewable chemicals, contributing to a more sustainable global economy. To develop predictive tools for the design and operation of industrially relevant strategies that utilize fermentative microbial communities, there is a need to…

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