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Tag: Phylum
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…
NifH database for taxonomic assignment in qiime2 – General Discussion
JThurston (Josh Thurston) January 19, 2024, 8:05pm 1 Hi all! I’m currently working through a Qiime2 pipeline analysing Illumina miseq paired-end amplicon data. I’ve successfully analysed bacterial (16s) amplicons from importing, filtering through to taxonomic assignment. However, I also have amplicon data for a functional gene (nifH; nitrogenase for N2…
Error produced when trying to assign taxonomy in DADA2 in R – rstudio
I have been trying to assign taxonomy against the MiDAS database in R. In previous steps, I have cleaned up my genetic data using the DADA2 profiles and then use this code to assign taxonomy taxa_midas_genus <- assignTaxonomy(seqtab.nochim, “C:/R/MiDAS.fa”, taxLevels = c(“Kingdom”, “Phylum”, “Class”, “Order”, “Family”, “Genus”), verbose = TRUE,…
Building the taxonomic profile of the Riniaie Marwah hot spring of Kishtwar in Jammu and Kashmir: the first high-throughput sequencing-based metagenome study
Background and objectives: Rinaie Marwah hot spring Kishtwar (RMHSK) is one of the geothermal springs located at 33°51’51″N 75°32’07″E with an elevation of 2134 meters above sea level in Jammu and Kashmir, India. We aimed to study the microbial diversity of this geothermal spring using metagenomics. Materials and methods: In…
Functional alterations and predictive capacity of gut microbiome in type 2 diabetes
Diversity and compositional analyses Regarding clinical differences (Table 1), T2DM individuals (mean 69.6 (± 12.3 sd) years) were significantly (p value < 0.01; Wilcoxon rank-sum test) older than the controls (46.9 (± 17.3 sd) years), showed higher BMI (mean 30.9 (± 7.01 sd) vs. mean 26.3 (± 6.12 sd) than the control…
Metagenome analyses identify human endogenous retrovirus-K113 (HML-2) subtype in glioblastoma
. 2023 Dec 15;133(24):e173959. doi: 10.1172/JCI173959. Item in Clipboard Amanda Macamo et al. J Clin Invest. 2023. Show details Display options Display options Format AbstractPubMedPMID . 2023 Dec 15;133(24):e173959. doi: 10.1172/JCI173959. Item in Clipboard Cite Display options Display options Format AbstractPubMedPMID No abstract available Keywords: Brain cancer; Oncology; Virology. PubMed Disclaimer…
Metagenomics-Based Characterization of Microbial Diversity across Indu
Environmental pollution is a serious concern that has been raised by rapid industrialization, urbanization, which in turn are associated with the problem of massive waste generation. Thousands of small and large industrial facilities dump their untreated waste into open land spaces or into local water resources. According to CPCB statistics…
The world’s largest proteins? These mega-molecules turn bacteria into predators
A structure prediction for a massive protein discovered by computational biologist Jacob West-Roberts and his colleagues.Credit: West-Roberts, J. et al./bioRxiv Jacob West-Roberts, a computational biologist at the University of California (UC) Berkeley, was scouring microbial DNA sequences for giant genes and discovered what he thought was a whopper: a gene…
LCA from BLAST output
LCA from BLAST output 1 I have a fairly large BLAST output from a metagenomics project with millions of lines per sample. The input sequences for the blast search were prodigal annotated proteins. I have been looking for a while now to find a suitable program that calculates the LCA…
SQL request from NCBI metadata and stat_analysis tables
I’m trying to do a SQL request on the BigQuery Google service to search for family names present in my sample DRR000836, and more precisly, on the cyanobacteria phylum part but I’m not sure how to do it… Here are the 2 SQL requests that I would like to merge…
Rare Microbes Discovered Living Inside the International Space Station
The cell size and colony morphology of all five novel species. Scanning Electronic Micrograph images of several novel bacterial species identified aboard the ISS in the Microbial Tracking studies. — Nature Rare microbes fill unique ecological niches and may hold blueprints for powerful new technologies like antibiotics. Now, a new…
Multi-omics analyses of gut microbiota via 16S rRNA gene sequencing, LC-MS/MS and diffusion tension imaging reveal aberrant microbiota-gut-brain axis in very low or extremely low birth weight infants with white matter injury | BMC Microbiology
Clinical features of WMI and nWMI groups From April 2022 to December 2022, the Affiliated Hospital of Guangdong Medical University enrolled a total of 83 subjects who met the inclusion criteria. The study finally included 71 cases after excluding 4 deaths, 6 patients who failed to complete MRI + DTI testing, 1…
Lower-limb ulcers in participants with leprosy sequelae
Introduction Leprosy is a disabling infectious disease that predominantly occurs in the skin and peripheral nerves and is transmitted by contact with pathogenic bacteria through the respiratory tract and broken skin. Leprosy is attributed to infection with Mycobacterium leprae (M. leprae)1 and the more recently discovered Mycobacterium lepromatosis.2 In addition,…
Marine toxin domoic acid alters nitrogen cycling in sediments
Effects of DA on potential N transformation rates It was reported that DIN in overlying water is mainly from sediments25, so the variation of DIN concentrations in overlying water was monitored, so as to infer the potential N transformation process in sediments. Generally, it can be observed that the overlying…
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,…
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…
Sequence-Based Classification and Identification | SpringerLink
Adékambi T, Drancourt M, Raoult D (2009) The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 17:37–45 CrossRef PubMed Google Scholar Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 CrossRef CAS PubMed Google Scholar Arahal DR,…
Obesity-resistant shrews can aid weight loss in mice
Globally, the prevalence of obesity has increased, which has had severe detrimental effects on physical health in recent years. Several hypotheses explain the causes of obesity. The change in people’s eating habits is one significant reason, with high-fat diets (HFD) being of particular concern. Research has indicated that the gut…
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…
Genome wide analysis revealed conserved domains involved in the effector discrimination of bacterial type VI secretion system
Construction of the VgrG database Encoded as a stand-alone gene or fused at the N-terminus of the toxin, the MIX domains can assist the delivery of their cognate T6SS effector19,20. As the central component of the spike complex, VgrG is a good marker to explore the potential conserved domains involved…
Fermentation | Free Full-Text | Whole-Genome Sequencing of Lactiplantibacillus plantarum YY-112 and Investigation of Its Immune-Modulating Abilities In Vivo
Author Contributions Conceptualization, Y.Y. and Y.G.; Data curation, M.L. and W.Z.; Formal analysis, M.L., W.Z., W.T. and J.L.; Funding acquisition, Y.Y. and Y.G.; Investigation, J.X., Y.Y. and Y.G.; Methodology, M.L., J.L. and Y.Y.; Project administration, Y.Y.; Resources, J.X., Y.Y. and Y.G.; Software, M.L., W.Z. and W.T.; Supervision, J.X., Y.Y. and…
The Mla system of diderm Firmicute Veillonella parvula reveals an ancestral transenvelope bridge for phospholipid trafficking
Bacterial strains and growth conditions Veillonella parvula SKV38 was grown in SK medium (10 g/L tryptone [Difco], 10 g/L yeast extract [Difco], 0.4 g/L disodium phosphate, 2 g/L sodium chloride, and 10 ml/L 60% [wt/vol] sodium DL-lactate; described in ref. 51. Cultures were incubated at 37 °C in anaerobic conditions, either in anaerobic bags (GENbag anaero;…
Taxonomic and environmental distribution of bacterial amino acid auxotrophies
Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008). Article ADS CAS PubMed Google Scholar Yu, X. J., Walker, D. H., Liu, Y. & Zhang, L. Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts. Infect. Genet. Evol….
Taxonomic identification and temperature stress tolerance mechanisms of Aequorivita marisscotiae sp. nov
Zain ul Arifeen, M., Ma, Y.-N., Xue, Y.-R. & Liu, C.-H. Deep-sea fungi could be the new arsenal for bioactive molecules. Mar. Drugs 18, 9 (2020). Article Google Scholar Martínez-Espinosa, R. M. Microorganisms and their metabolic capabilities in the context of the biogeochemical nitrogen cycle at extreme environments. Int. J….
EMDB < EMD-14025
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Using 16S rDNA and metagenomic sequencing technology to analyze the fecal microbiome of children with avoidant/restrictive food intake disorder
Patient demographics Among the children, 102 were diagnosed with ARFID, and 33 were healthy. There were 50 males and 52 females in the ARFID group and 15 males and 18 females in the healthy control group (HC group). There was no significant difference in age (P = 0.352) or sex composition (P = 0.512)….
EMDB < EMD-16930
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Metaproteogenomic analysis of saliva samples from Parkinson’s disease patients with cognitive impairment
Characteristics of participants and analyses A total of 115 individuals (43 PDD, 45 PD-MCI) and 27 HC were included in this study. Both 16 S rRNA gene amplicon sequencing based microbiome analysis and metaproteomics profiling were performed for all salivary samples collected from the participants (Fig. 1). Fig. 1: Experimental overview….
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…
Solved Use phyloseq for this question. Here is the dataset:
Use phyloseq for this question. Here is the dataset: [1] “BW1_sub_R1_trimmed.fq” “BW1_sub_R2_trimmed.fq” [3] “BW2_sub_R1_trimmed.fq” “BW2_sub_R2_trimmed.fq” [5] “filtered” “R10_sub_R1_trimmed.fq” [7] “R10_sub_R2_trimmed.fq” “R11_sub_R1_trimmed.fq” [9] “R11_sub_R2_trimmed.fq” “R11BF_sub_R1_trimmed.fq” [11] “R11BF_sub_R2_trimmed.fq” “R12_sub_R1_trimmed.fq” [13] “R12_sub_R2_trimmed.fq” “R1A_sub_R1_trimmed.fq” [15] “R1A_sub_R2_trimmed.fq” “R1B_sub_R1_trimmed.fq” [17] “R1B_sub_R2_trimmed.fq” “R2_sub_R1_trimmed.fq” [19] “R2_sub_R2_trimmed.fq” “R3_sub_R1_trimmed.fq” [21] “R3_sub_R2_trimmed.fq” “R4_sub_R1_trimmed.fq” [23] “R4_sub_R2_trimmed.fq” “R5_sub_R1_trimmed.fq” [25] “R5_sub_R2_trimmed.fq” “R6_sub_R1_trimmed.fq” [27] “R6_sub_R2_trimmed.fq”…
Microbiome study of a coupled aquaponic system: unveiling the independency of bacterial communities and their beneficial influences among different compartments
Grey mullet (family Mugilidae) farming has a tradition of several hundred years both in Oriental and Western countries in extensive and semi-intensive systems; however, there is still scarce information about their performance and nutritional requirements under different rearing systems and conditions28. This group of euryhaline and eurythermal species is generally…
Additional file 1 of Anti-diarrheal drug loperamide induces dysbiosis in zebrafish microbiota via bacterial inhibition
journal contribution posted on 2023-11-12, 04:20 authored by Rebecca J. Stevick, Bianca Audrain, Sébastien Bedu, Nicolas Dray, Jean-Marc Ghigo, David Pérez-Pascual Additional file 1: Supplementary figures: Fig. S1. Sequencing depth and coverage for 16S rRNA gene amplicon data from conventional zebrafish larvae. (A) Number of quality-controlled bacterial sequences per sample. (B)….
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…
Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae
Sheridan, P. O. et al. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat. Commun. 11, 1–12 (2020). Article Google Scholar Sheridan, P. O., Meng, Y., Williams, T. A. & Gubry-Rangin, C. Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat. Commun. 13, 1–13…
Recovery of microbial DNA by agar-containing solution from extremely low-biomass specimens including skin
Ethical considerations This study complies with relevant institutional, national, and international guidelines and legislation. The Ethics Committee at the RIKEN Center for Integrative Medical Sciences (H30-4) approved this study, and written informed consent was obtained from all volunteers who provided specimens. Sampling solutions The AgST solution was prepared as follows:…
Comprehensive 16s rRNA sequencing and metabolomics to investigate the effect of anticancer bioactive peptides combined with oxaliplatin on gastric cancer
Background: The occurrence and development of gastric cancer are closely related to the gut microbiota. Previous studies have found that the combination of anticancer bioactive peptides (ACBP) and oxaliplatin (OXA) has a significant therapeutic effect on gastric cancer. However the impact of ACBP-OXA on the gut microbiota was still unclear….
EMDB < Search results
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
ASMT determines gut microbiota and increases neurobehavioral adaptability to exercise in female mice
Female Asmt ft/ft mice exhibits anxiety- and depression-like behaviors We first examined the anxiety- and depression-like behaviors in mice. Our results showed that female Asmtft/ft mice had less distance in center (p < 0.001) and a smaller number of poking (p < 0.05) in the open field test (OFT, Fig. 1a–c). In the forced swim…
Dataset for metagenomic analysis of bacterial community grown in sediments contaminated with pulp paper mill waste pollutants
Published: 6 November 2023| Version 2 | DOI: 10.17632/gpmwyfhbp3.2 Contributors: Vineet Kumar, Pradeep Verma Description Pulp and paper mills (PPMs) generate complex and recalcitrant chlorolignin pollutants in their waste stream, posing a significant environmental and health threat. To understand how microbial communities can help in the clean-up of chlorolignin waste…
Oral microbiota bounces back five years after quitting smoking
In a recent study published in the journal Scientific Reports, researchers examined the changes in oral microbiota composition due to smoking. Smoking is a risk factor for cardiovascular diseases, oropharyngeal cancers, periodontitis, and respiratory diseases, among others. Oral microbiota alterations have been reported in smokers and cases of periodontitis, cardiovascular…
Mutational spectra are associated with bacterial niche
Bacteria exhibit diverse mutational spectra Using a specifically-developed open-source bioinformatic tool, MutTui (github.com/chrisruis/MutTui), we analysed whole genome sequence alignments and phylogenetic trees to reconstruct single base substitution (SBS) mutational spectra of 84 phylogenetic clades from 31 diverse bacterial species representing a broad range of phylogenetic diversity and replication sites (Figs. S1…
Wolbachia dominance influences the Culex quinquefasciatus microbiota
In this work, bacterial and fungal microbiome from two laboratory Cx. quinquefasciatus isolines (wt and -tet) were compared throughout mosquito development, including changes in female feeding. Bacterial communities in the wt line presented higher Shannon diversity in larvae than adults, as has been demonstrated in a Wolbachia carrier Ae. albopictus…
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…
The metagenomic and metabolomic profile of the gut microbes in Chinese full-term and late preterm infants treated with Clostridium butyricum
Ethics approval and consent to participate The study was approved by the Human Research Ethics Committees of the Children’s Hospital of Soochow University (Reference 2020CS017). All specimens were collected according to the guidelines set by the Children’s Hospital of Soochow University. All authors confirm that all methods were performed in…
EMDB < EMD-40454
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Spatial compartmentalisation of bacteria in phoronid microbiomes
Phoronids, or horseshoe worms (phylum Phoronida), are marine invertebrates whose life cycle usually involves a pelagic larva and a benthic, sessile adult that bores into soft sediment or hard substrates like rocks or mollusc shells1. Phoronids filter-feed using an arch of tentacles, the lophophore, and protect their vermiform trunk with…
Orange juice containing Pediococcus acidilactici CE51 modulates the intestinal microbiota and reduces induced inflammation in a murine model of colitis
In view of the need for studies on compounds that act in the treatment and prevention of ulcerative colitis, this study evaluated and found the positive effect of the probiotic drink containing P. acidilactici CE51 regarding the reduction of inflammatory parameters presented in histopathological analyzes and modulation of the gut…
Microbiomes associated with Coffea arabica and Coffea canephora in four different floristic domains of Brazil
General information In total, more than 60 million reads were obtained: 30,700,327 for 16S rDNA/bacteria and 29,920,072 for ITS/fungi. These sequences were distributed across more than 1000 bacterial and fungal genera (Fig. 2). The coverage index10 was above 0.95 for all samples, showing that the sequencing effort was enough to capture…
Wastewater sequencing reveals community and variant dynamics of the collective human virome
Probe-based capture drives viral enrichment We developed a comprehensive viral capture approach using a diverse probe set across ten different sites on a weekly basis for nearly 1 year. The probes (TWIST Comprehensive Viral Capture Panel) are directed against a panel of 3153 different human and animal virus genomes. As part…
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…
Biological fingerprints in soil show where diamond-containing ore is buried
Soil microbial community composition, diversity, and indicator species for the kimberlite amendment experiment. a Distribution of 16 S rRNA gene reads per phylum for each sample. The number of reads per phylum is calculated as a percentage of the total reads for each sample. The “other” grouping represents phyla that when summed…
Identification and cultivation of anaerobic bacterial scavengers of dead cells
Bar-On YM, Phillips R, Milo R. The biomass distribution on Earth. Proc Natl Acad Sci USA. 2018;115:6506–11. Article CAS PubMed PubMed Central Google Scholar Ogawa H, Amagai Y, Koike I, Kaiser K, Benner R. Production of refractory dissolved organic matter by bacteria. Science. 2001;292:917–20. Article CAS PubMed Google Scholar Liang…
EMDB < EMD-25228
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Uncovering the relationship between gut microbial dysbiosis, metabolomics, and dietary intake in type 2 diabetes mellitus and in healthy volunteers: a multi-omics analysis
After processing the data, 20 control samples and 21 Type 2 Diabetes Mellitus samples contained data from all three collected assays (bacteriome, mycobiome, metabolome). The bacteriome data comprised on average 9534 contigs (s.d. ± 3465), ranging from 2032 to 18,320 contigs (786 ASVs). The mycobiome data contained on average 5450 contigs (s.d. ± 4964),…
New research finds marine bacteria ditched their flagella and other traits when migrating back to the ocean
The JGI worked with researchers from the University of Nevada, Las Vegas to sequence Dehalococcoidia isolate genomes from the Great Boiling Spring in Nevada. Credit: Jonathan K. Covington Scientists have discovered flagella in an unexpected place: hot spring-dwelling bacteria from the phylum Chloroflexota. Research shows that flagella were lost in…
Microbiology – Module 6 – ATYPICAL BACTERIA ^includes species identified in 16 s rRNA and rDNA and
ATYPICAL BACTERIA – ^includes species identified in 16s rRNA and rDNA and metagenomics (field that studies diff genes in a particular sample) ●Metagenomics – Ex. You have a soil specimen and you want to identify the diff organisms so you extract the DNA and do 16s rRNA gene amplification and…
Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle
Falkowski P. G., Raven J. A. Aquatic Photosynthesis (Princeton Univ. Press, 2013). Sanchez-Baracaldo, P., Bianchini, G., Wilson, J. D. & Knoll, A. H. Cyanobacteria and biogeochemical cycles through earth history. Trends Microbiol. 30, 143–157 (2022). Article CAS PubMed Google Scholar Blankenship, R. E. Early evolution of photosynthesis. Plant Physiol. 154,…
Diabetic Foot Ulcer and the Bacterial Colony of the Skin
Introduction Diabetes is a growing public health problem with increasing prevalence and mortality that threatens the health of people globally.1 In 2021, the global prevalence of diabetes in adults aged 20 to 79 years was estimated at 537 million, mainly caused by type 2 diabetes, and the number is expected…
Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium
Rabus, R., Hansen, T. A. & Widdel, F. In Dissimilatory Sulfate-and Sulfur-Reducing Prokaryotes. The Prokaryotes: Prokaryotic Physiology and Biochemistry, Rosenberg E., DeLong E. F., Lory S., Stackebrandt E., and Thompson F. at (2013). Rabus, R. et al. Chapter Two—A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing…
Encountering unknown error in ancom – Technical Support
Hello fellow qiime2 users,I’ve been trying to figure out differentially abundant microbial population in diabetic patients but facing so many obstacles that I can’t figure out alone as a novice metagenomic analyst, so I need your help and I’m attaching all the files I used and errors I got below….
G. lucidum triterpenes restores intestinal flora balance in non-hepatitis B virus-related hepatocellular carcinoma: evidence of 16S rRNA sequencing and network pharmacology analysis
. 2023 Sep 18:14:1197418. doi: 10.3389/fphar.2023.1197418. eCollection 2023. Affiliations Expand Affiliation 1 Chongqing Three Gorges Medical College, Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Chongqing, China. Free PMC article Item in Clipboard Wei Xiong et al. Front Pharmacol. 2023. Free PMC article…
18S taxonomy assignment SILVA database formatting
Hi Bioinformatic community, I would like to classify 18S data (V7) of Fungi with assignTaxonomy from dada2. For that I downloaded SILVA_132_SSURef_tax_silva.fasta.gz from the SILVA website and need to format it, what I do with some Linux command line oneliner. But some species in the database have a different number…
Metagenomic insight into precipitation processes in microbial communities from salar de Atacama
Título del Libro: Libro de Resúmenes del XVII Congreso Argentino de Microbiología General Resumen The Salar de Atacama is one of the Earth’s largest evaporite basins (ca. 3,000 km2). Within this large area, numerous hypersaline lakes can be found. These lakes are hotspots for microbial diversity, and diverse structures with…
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…
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…
Effects of a postbiotic SLFC non scalp microbiome
Introduction Sensitive scalp is a skin syndrome caused by the hyper-reactivity to environmental stimuli, which might cause inflammatory symptoms and abnormal sensory reactions of the scalp including pruritus, prickling, tightness, pain, and burning, but without visible signs of inflammation.1 Various circumstances, such as the atmospheric environment, heat, pollution, hair care…
Feeding pigs liquid whey positively affects faecal microbiota
The pig gut microbiota composition and diversity shift over time and along the entire gut tract. In the swine industry, liquid-feeding products positively contribute to the equilibrium of animal guts, thus supporting the reduction of feed medication. Liquid whey, a by-product of cheese-making, contains all the essential amino acids of…
Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts
Study population Among the 60 cases, 28 were male (46.7%) and 32 were female (53.3%) ranging between 1.5 and 90 years of age; most patients were between 19 and 64 years (n = 26; 43.3%) or less than 9 years (n = 16; 26.7%). No difference in the proportion of stool submissions was observed by year, though…
Integrated meta-omics approaches reveal Saccharopolyspora as the core functional genus in huangjiu fermentations
Saccharopolyspora is abundant in the wheat qu and HJFM microbiota To uncover the variation curve of microorganisms during fermentation, microbial DNA copy numbers and community structure were analyzed using quantitative real-time PCR (qPCR) and metagenomic analyses. DNA copy numbers of total bacteria and fungi in wheat qu were 11.2 ± 0.2 log10…
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…
Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae
Brocks, J. J. et al. The rise of algae in Cryogenian oceans and the emergence of animals. Nature 548, 578–581 (2017). Article ADS CAS PubMed Google Scholar Leliaert, F. Green algae: Chlorophyta and Streptophyta. In Encyclopedia of microbiology 457–468 (Academic Press, 2019). Zhang, Z. et al. Origin and evolution of…
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…
Gut Microbiome of Children with Airway Allergic Disease
Introduction Allergic airway diseases affect many people worldwide, and incidences are still increasing gradually. Allergic rhinitis and allergic asthma, are typical chronic nasopharyngitis respiratory diseases in pediatric, causing an enormous burden of illness and high economic costs to the community.1 Allergic rhinitis and allergic asthma are immunoglobulin E (IgE)-mediated inflammatory…
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…
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….
Deep-Sea Hydrothermal Vents Harbor a New Species of Marine Bacteria With Bioactive Properties
The deep sea is a vast and mysterious realm that harbors a rich diversity of life forms, many of which are still unknown to science. Among these are the Planctomycetes, a group of bacteria that have unique features and play important roles in various biogeochemical cycles. Recently, researchers have discovered…
Emergence of putative energy parasites within Clostridia revealed by genome analysis of a novel endosymbiotic clade
Cryan JF, O’Riordan KJ, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, et al. The microbiota-gut-brain axis. Physiol Rev. 2019;99:1877–2013. Article CAS PubMed Google Scholar Lopetuso LR, Scaldaferri F, Petito V, Gasbarrini A. Commensal clostridia: leading players in the maintenance of gut homeostasis. Gut Pathog. 2013;5:e23. Article Google Scholar Collins…
Comparison of 16S rRNA gene sequencing microbiota among children with serological IgE-mediated food hypersensitivity
Background: We hypothesized that specific food hypersensitivity (FH) in children is linked to specific gut microbiota. The aim of our study was to quantify and evaluate differences in gut microbial composition among children with different IgE-mediated FH. Methods: Children (n = 81) aged 18 to 36 months were enrolled, fecal…
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…
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…
EMDB < EMD-40539
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data
Publicly available mock community sequencing datasets 136 mock community sequencing samples were collected in total from four publicly available sequencing datasets and analyzed in our evaluation. 69 samples are from Lluch et al.33; 33 samples are from Kozich et al.34; 29 samples are from Fouhy et al.35; and 5 samples…
Microorganisms | Free Full-Text | Genome-Wide and 16S rRNA Sequencing-Based Analysis on the Health Effects of Lacticaseibacillus paracasei XLK401 on Chicks
1. Introduction Since 2006, the European Union has prohibited the use of antibiotics in animal feed to boost growth [1]. This ban has resulted in a significant rise in disease outbreaks in broiler farming [2]. Therefore, there is an urgent need to find effective antibiotic alternatives for use in the…
Effect of a microencapsulated probiotic on the intestinal microbiome of Pacific white shrimp
21 August 2023 Chung-Hung Liu Microencapsulation of Bacillus subtilis E20 proved effective in addressing probiotic issues related to inclusion during feed manufacturing Results of this study showed that microencapsulation was effective in addressing probiotic issues related to inclusion during feed manufacturing, that encapsulated B. subtilis E20 administration increased beneficial strains…
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…
Inter-comparison of marine microbiome sampling protocols
Environmental communities For the MetaB16SV4V5 sequencing results (n = 60), we initially obtained between 714,103 and 2,841,890 raw reads per sample (median = 1,462,584 reads, IQR = 267,472 reads). The final number of high quality reads attributed to taxonomic lineages ranged between 169,945 and 1,517,860 reads per sample (median = 660 878 reads, IQR = 438 932 reads). Thus, between…
Comparative genomics unveils extensive genomic variation between populations of Listeria species in natural and food-associated environments
Core genomes of Listeria species strongly differ between natural and food-associated environments and can accurately predict isolation sources at a lineage level To assess the relationship between the core genome of L. monocytogenes (which entails genomes of all three L. monocytogenes lineages identified in this study – lineage I, II,…
Struktur Komunitas dan Aktivitas Bakteri Nitrifikasi, Denitrifikasi, dan Nitrat Amonifikasi di Tambak Udang Sistem Intensif
Udang merupakan salah satu komoditas unggulan perikanan budidaya di Indonesia. Tambak udang sebagai suatu ekosistem memiliki senyawa nitrogen anorganik utama yang dapat terlarut dalam air, yaitu amonia (NH3), nitrat (NO3-), dan nitrit (NO2-). Permasalahan yang sering terjadi dalam pengelolaan tambak udang yaitu penurunan kualitas air dan sedimen yang disebabkan oleh…
Well-hidden methanogenesis in deep, organic-rich sediments of Guaymas Basin
Magnabosco C, Lin LH, Dong H, Bomberg M, Ghiorse W, Stan-Lotter H, et al. The biomass and biodiversity of the continental subsurface. Nat Geosci. 2018;11:707–17. Article CAS Google Scholar LaRowe DE, Amend JP. Catabolic rates, population sizes and doubling/replacement times of microorganisms in natural settings. Am J Sci. 2015;315:167–203. Article …
Metagenomic analysis of soybean endosphere microbiome to reveal signatures of microbes for health and disease | Journal of Genetic Engineering and Biotechnology
Sequencing quality analysis To process the metagenome data analysis, dataset quality analysis was performed using the FastQC program. The FastQC program provides a QC report on spot problems that originate either in the sequencer or in the starting library material. Many modules were used to evaluate the raw data, and…
Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle
Bond PL, Hugenholtz P, Keller J, Blackall LL. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl Environ Microbiol. 1995;61:1910–6. Article CAS PubMed PubMed Central Google Scholar Wang Z, Guo F, Liu L, Zhang T. Evidence of carbon fixation pathway in a bacterium from candidate…
The effects of Selenohomolanthionine supplementation on the rumen eukaryotic diversity of Shaanbei white cashmere wether goats
Rumen eukaryotic diversity The 18s rRNA gene sequencing experiment of 32 Shaanbei white cashmere wether goat rumen fluid samples produced a total of 2,623,541 reads with an average of 81,985.66 ± 765.86 [(mean ± standard error of the mean (SEM), n = 32] per sample. A total of 3,123 operational taxonomic units (OTUs) were obtained based…
EMDB < EMD-12919
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria
Baumgartner, K., Coetzee, M. P. A. & Hoffmeister, D. Secrets of the subterranean pathosystem of Armillaria: subterranean pathosystem of Armillaria. Mol. Plant Pathol. 12, 515–534 (2011). Article PubMed PubMed Central Google Scholar Heinzelmann, R. et al. Latest advances and future perspectives in Armillaria research. Can. J. Plant. Pathol. 41, 1–23…
Assessment of prokaryotic communities in Southwestern Atlantic deep-sea sediments reveals prevalent methanol-oxidising Methylomirabilales
Romans, B. W. & Graham, S. A. A deep-time perspective of land–ocean linkages in the sedimentary record. Annu. Rev. doi.org/10.1146/annurev-marine-121211-172426 (2013). Article Google Scholar Smith, S. V. & Hollibaugh, J. T. Coastal metabolism and the ocean organic carbon balance. Rev. Geophys. 31, 75–89 (1993). Article ADS Google Scholar Bauer, J….
MPs | Free Full-Text | Comparative Analysis of Primers Used for 16S rRNA Gene Sequencing in Oral Microbiome Studies
1. Introduction Microbiota are found in many habitats but are poorly characterized due to a high proportion of unnamed species-level taxa [1,2]. However, the human oral bacterial community is relatively well characterized at the species level and boasts many types of microbiota. In fact, the oral cavity is second only…
Solved 42. The relative amount of Firmicutes is higher in
42. The relative amount of Firmicutes is higher in conventional mice treated with the high-fat diet compared to the low-fat diet. True False 43. Diet is not a selective pressure on the microbiome of conventional mice. True False 44. The ability to absorb different nutrients varies from one bacterium to…
Late acquisition of the rTCA carbon fixation pathway by Chlorobi
Ward, L. M. & Shih, P. M. The evolution and productivity of carbon fixation pathways in response to changes in oxygen concentration over geological time. Free Radic. Biol. Med. 140, 188–199 (2019). Article CAS PubMed Google Scholar Hartman, H. Speculations on the origin and evolution of metabolism. J. Mol. Evolution…
3 Domains of Life (Bacteria, Archaea, Eukarya)
The primitive living world was classified into two primary domains of Eukaryotes (Eukarya) and Prokaryotes (Bacteria) based on microscopic characteristics such as the presence or absence of membrane-bound nuclei and other cellular organelles. In 1977, American microbiologist and physicist Carl Richard Woese and his co-workers discovered the third domain of…
16S rRNA gene primer choice impacts off-target amplification in human gastrointestinal tract biopsies and microbiome profiling
The problem of off-target amplification The widely used standardized protocol for 16S rRNA gene amplicon sequencing7,14 turned out to be inadequate due to robust off-target amplification of human DNA during the analysis of bacteriome in samples of different biopsy sites from the upper gastrointestinal (GI) tract. In samples from all…