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opencc-by-4.0Apr 2024View details →

Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts

Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By employing virome-enriched long-read metagenomics sequencing across 91 individuals, we identified a total of 14,438 non-redundant phage SVs, and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Strikingly, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibits a higher frequency of genetic exchange with bacterial chromosomes then virulent phages. Collectively, our findings provide novel insights into the genetic landscape of the human gut phageome.

opencc-by-4.0Oct 2024View details →

Aggregating gut: on the link between neurodegeneration and bacterial functional amyloids - Datasets

This repository contains data from work "Aggregating gut: on the link between neurodegeneration and bacterial functional amyloids" <a href="https://zenodo.org/api/records/14016809/draft/files/BFA.fasta/content" target="_blank" rel="noopener noreferrer">BFA.fasta</a> - fasta file containing sequences of bacterial functional amyloids used as a query for identification of novel bacterial functional amyloids in UHGP dataset <a href="https://zenodo.org/api/records/14016809/draft/files/UHGPAmyloids.fasta/content" target="_blank" rel="noopener noreferrer">UHGPAmyloids.fasta </a>- fasta file containing sequences of amyloids identified in UHGP dataset <a href="https://zenodo.org/api/records/14016809/draft/files/UHGPAmyloids.csv/content" target="_blank" rel="noopener noreferrer">UHGPAmyloids.csv</a> - csv file containing information about amyloids identified in UHGP Columns: query_id - Uniprot id of the protein from BFA query_gene_name - gene name of the protein from BFA target_id - UHGP id of the found homolog ProbabilityAMYPred-FRL - score obtained for the target_id sequence according to AMYPred-FRL Archcandy - Prediction of beta arch motif for identified amyloid Genome - UHGP genome id of the target_id Localization - predicted subcellular localization with BUSCA for target_id sequence Lineage - full taxonomy of the target_id sequence (which bacteria produced this specific sequence)  <a href="https://zenodo.org/api/records/14016809/draft/files/PPIPositivePredictionsBetween_UHGPAmyloids_And_HPAIntestine_filtered.csv/content" target="_blank" rel="noopener noreferrer">PPIPositivePredictionsBetween_UHGPAmyloids_And_HPAIntestine_filtered.csv</a> - csv file contining inforamtions about predicted protein-protein interactions between UHGPAmyloids and human proteins expressed in guts Columns: UHGPAmyloids_id - UHGPAmyloids id (same as target_id in UHGPAmyloids.csv) hp_uniprot_name - Uniprot name of a human protein negative and score - scores returned by ProteinPrompt softwawre for prediction of PPI hp_uniprot_id - Uniprot id of a human protein BFA_sp_uniprot_id - Uniprot id of a BFA source protein BFA_sp_uniprot_name - gene name of a BFA source protein UHGPAmyloids_localization  - predicted subcellular localization with BUSCA for UHGPAmyloids_id sequence UHGPAmyloids_lineage - full taxonomy of the UHGPAmyloids_id sequence (which bacteria produced this specific sequence)

opencc-by-4.0Dec 2022View details →

The gut microbiota affects the social network of honey bees

This dataset contains input files needed to reproduce the automated behavioral tracking data analyses of the research article "The gut microbiota affects the social network of honey bees”. Codes using these data and additional datasets are available at: https://github.com/JoanitoLiberti/The-gut-microbiota-affects-the-social-network-of-honey-bees/

opencc-by-4.0Feb 2022View details →

Obesity reshapes the microbial population structure along the gut-liver-lung axis in mice

Data repository for the paper: Galaris A., Fanidis D. et al. Obesity reshapes the microbial population structure along the gut-liver-lung axis in mice. 2021 For further data requests and questions please contact the corresponding author of the respective publication. All fastq files have been processed to remove human and mouse sequences.

opencc-by-4.0Sep 2021View details →

Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: viruses, plasmids, and more

S1 Data Dataset including the discovered CRISPR spacers, direct repeats, protospacers, co-occurrence-based spacer clustering results, predicted protein sequences, built HMMs, database comparison results, phylogenetic analysis results, predicted targeting hosts, and CRISPR-targeted TR sequences.

opencc-by-4.0Dec 2023View details →

Strains used in the paper "Bacteriophage cultivation for commensal human gut bacteria"

Sequences of 16S rRNA genes of 411 strains for taxonomic detection; Genomic sequence of of 42 strains for taxonomic detection; Genomic sequence of Bacteroides fragilis and Parabacteroides merdae strains used for genomic analysis in phage-host range analysis experiments.

opencc-by-4.0Sep 2022View details →

Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics

In the human gut, the growth of Clostridioides difficile is impacted by a complex web of inter-species interactions with members of human gut microbiota. We investigate the contribution of inter-species interactions on the antibiotic response of C. difficile to clinically relevant antibiotics using bottom-up assembly of human gut communities. We discover two classes of microbial interactions that alter C. difficile’s antibiotic susceptibility: infrequent increases in tolerance at high antibiotic concentrations and frequent growth enhancements at low antibiotic concentrations. Based on genome-wide transcriptional profiling data, we demonstrate that metal sequestration due to hydrogen sulfide production by the prevalent gut species Desulfovibrio piger increases metronidazole tolerance of C. difficile. Competition with species that display higher sensitivity to the antibiotic than C. difficile leads to enhanced growth of C. difficile at low antibiotic concentrations. A dynamic computational model identifies the ecological design principles driving this effect. Our results provide a deeper understanding of ecological and molecular principles shaping C. difficile’s response to antibiotics, which could inform therapeutic interventions.

opencc-by-4.0Sep 2022View details →

Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics

opencc-by-4.0Mar 2022View details →

Genome of the isolates: Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities

The draft genome of the isolates in Mouse Intestinal Bacteria Collection (miBC)   Microbiome research is hampered by the fact that many bacteria are still unknown and by the lack of publicly available isolates. Fundamental and clinical research is in need of comprehensive and well-curated repositories of cultured bacteria from the intestine of mammalian hosts. Due to host-specific features of the gut microbiota, it is sound to establish collections of isolates from single host species. Hence, this project established a collection of bacterial strains isolated from the intestine of mice. The original version of the collection published in 2016 (Lagkouvardos, et. al. 2016. Nat. Microbiol.). was doubled by the addition of 112 strains, representing a total of 141 species across 6 phyla and 35 families for the entire collection. As we aimed to create a well-curated resource, all bacterial species within miBC have been taxonomically described and are publicly available.

opencc-zeroOct 2022View details →

The gut microbiome reflects ancestry despite dietary shifts across a hybrid zone

The microbiome is critical to an organism's phenotype, and its composition is shaped by, and a driver of, eco-evolutionary interactions. We investigated how host ancestry, habitat, and diet shape gut microbial composition in a mammalian hybrid zone that occurs across an ecotone between distinct vegetation communities. We found that habitat is the primary determinant of diet, while host genotype is the primary determinant of the gut microbiome—a finding further supported by intermediate microbiome composition in first generation hybrids. Despite these distinct primary drivers, microbial richness was correlated with diet richness, and individuals that maintained higher dietary richness had greater gut microbial community stability. Both relationships were stronger in the relative dietary generalist of the two parental species. Our findings show that host ancestry interacts with dietary habits to shape the microbiome, ultimately resulting in the organismal phenotypic plasticity that host-microbial interactions allow.

opencc-zeroMay 2024View details →

Data from: Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population

In humans, gut microbiome (GM) differences are often correlated with, and sometimes causally implicated in, ageing. However, it is unclear how these findings translate in wild animal populations. Studies that investigate how GM dynamics change within individuals, and with declines in physiological condition, are needed to fully understand links between chronological age, senescence, and the GM, but have rarely been done. Here, we use longitudinal data collected from a closed population of Seychelles warblers (Acrocephalus sechellensis) to investigate how bacterial GM alpha diversity, composition, and stability are associated with host senescence. We hypothesised that GM diversity and composition will differ, and become more variable, in older adults, particularly in the terminal year prior to death, as the GM becomes increasingly dysregulated due to senescence. However, GM alpha diversity and composition remained largely invariable with respect to adult age and did not differ in an individual's terminal year. Furthermore, there was no evidence that the GM became more heterogenous in senescent age groups (individuals older than 6 years), or in the terminal year. Instead, environmental variables such as season, territory quality, and time of day, were the strongest predictors of GM variation in adult Seychelles warblers. These results contrast with studies on humans, captive animal populations, and some (but not all) studies on non-human primates, suggesting that GM deterioration may not be a universal hallmark of senescence in wild animal species. Further work is needed to disentangle the factors driving variation in GM-senescence relationships across different host taxa.

opencc-by-4.0Sep 2024View details →

Figure 2 in Isolation and characterization of bacteria associated with silkworm gut under antibiotic-treated larval feeding

Figure 2. Phylogenetic relationship and identification of bacterial strains isolated in this study based on 16S rRNA gene sequence through Neighbor Joining method using 1000 bootstrap replicates.

opencc-zeroJun 2024View details →

Dataset: Fractyl Health, Inc. (GUTS) Stock Performance

This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.

opencc-zeroJul 2024View details →

Data from: Gut-resident microorganisms and their genes are associated with cognition and neuroanatomy in children

The gastrointestinal tract, its resident microorganisms, and the central nervous system are connected by biochemical signaling, also known as the "microbiome-gut-brain-axis." Both the human brain and the gut microbiome have critical developmental windows in the first years of life, raising the possibility that their development is co-occurring and likely co-dependent. Emerging evidence implicates gut microorganisms and microbiota composition in cognitive outcomes and neurodevelopmental disorders (e.g., autism and anxiety), but the influence of gut microbial metabolism on typical neurodevelopment has not been explored in detail. We investigated the relationship of the microbiome with the neuroanatomy and cognitive function of 381 healthy children, demonstrating that differences in gut microbial taxa and gene functions are associated with overall cognitive function and with differences in the size of multiple brain regions. Using a combination of multivariate linear and machine learning (ML) models, we showed that many species, including Alistipes obesi and Blautia wexlerae, were associated with higher cognitive function, while some species such as Ruminococcus gnavus were more commonly found in children with low cognitive scores after controlling for sociodemographic factors. Microbial genes for enzymes involved in the metabolism of neuroactive compounds, particularly short-chain fatty acids such as acetate and propionate, were also associated with cognitive function. In addition, ML models were able to use microbial taxa to predict the volume of brain regions, and many taxa that were identified as important in predicting cognitive function also dominated the feature importance metric for individual brain regions, and for specific subscales of cognitive function. For example, B. wexlerae was the most important species in models predicting the size of the parahippocampal region in both the left and right hemispheres and was among the top predictors of gross motor and expressive language performance. Several species from the phylum Bacteroidetes, including GABA-producing Bacteroides ovatus, were important for predicting the size of the left accumbens area, but not the right. These findings provide potential biomarkers of neurocognition and brain development and may lead to the future development of targets for early detection and early intervention.

Figure 1 in Angiostrongylus cantonensis cathepsin B-like protease (Ac-cathB-1) is involved in host gut penetration

Figure 1. Selection and identification of the stably expressed cell line. (A) Schematic diagram of vector construction. Replacement of the GFP with a sequence containing 50 IgK SP and 30 myc-His sequence using an isocaudamer technique resulted in the creation of pBobi-IMHIP vector. Lentiviral vector pBobi-cathB1 was generated by insertion of Ac-cathB-1 coding sequence excluding SP into the pBobi-IMHIP vector by XbaI and BamHI restriction sites. (B) Lentiviral packaging of pBobi-cathB1 and pBobi-GFP. Under the fluorescence microscope, more than 90% of cells in the pBobi-GFP transfected group displayed green fluorescence. (C) Assessment of the establishment of 293T-cathB1. Anti-Myc IF staining was performed in the two cell lines. All cells in 293T-cathB1 showed red fluorescence representing 100% positive, while all cells in 293T-GFP showed no fluorescence under the red fluorescent filter due to the lack of myc-tag expression. (D) Tests for rAccathB-1 expression. Total RNA and protein samples were extracted from two groups of cells. Results of RT-PCR (top two panels) and western blot (lower two panels) showed that rAc-cathB-1 was highly expressed in 293T-cathB1 at both mRNA and protein levels. Actb, RT-PCR control and B-actin, loading control for western blot; WL, white light; and bar = 100 µm.

Figure 2 in Angiostrongylus cantonensis cathepsin B-like protease (Ac-cathB-1) is involved in host gut penetration

Figure 2. Purification and identification of rAc-cathB-1. (A) Purification of rAc-cathB-1 from the cell culture supernatant. Lanes: MW, molecular weight markers (listed in kDa on the side); 1, concentrated culture supernatant in binding buffer; 2, column flowthrough; 3, binding buffer wash; 4–6, successive eluate fractions (during the elution step, the eluate was collected in one 5 ml tube after another); 7, eluate from gel filtration. (B) Identification of purified rAc-cathB-1 by western blot with an antiserum against Ac-cathB-1 expressed in E. coli and an anti-Myc antibody.

Figure 5 in Angiostrongylus cantonensis cathepsin B-like protease (Ac-cathB-1) is involved in host gut penetration

Figure 5. Effects of antiserum on the hydrolytic activity of activated rAc-cathB-1 and larval gut penetration. (A) The inhibition of activated rAc-cathB-1 by antiserum. One microgram of rAc-cathB-1 was activated and incubated with the positive serum (6.0 µg) or negative serum (6.0 µg) for 30 min, respectively, prior to assessment of the degradation of Z-RR-AMC. The hydrolytic reaction was performed at 37 °C for 30 min and the fluorescence of released AMC was measured. All data were presented as relative activities of activated rAc-cathB-1, where the activity of the control (without serum treatment) was taken as 100%. (B) Inhibition of larval penetration ability. Two hundred L3 larvae were pretreated with the undiluted positive serum, the undiluted negative serum, or PBS at 37 °C for 30 min, respectively. The three groups of larvae were separately injected into lumens of rat gut sacks and kept in sterilized Tyrode's solution at 37 °C for 3 h. Each trial was conducted in triplicate and the numbers of larvae remaining in the gut lumen were counted. Numbers of L3 that penetrated the isolated gut were calculated and presented as indicated. Asterisk (*), P <0.05; ns, not significant.

Figure 4 in Angiostrongylus cantonensis cathepsin B-like protease (Ac-cathB-1) is involved in host gut penetration

Figure 4. Assessment of the hydrolytic activity of activated rAc-cathB-1. (A) Activated rAc-cathB-1 completely degraded fibronectin and laminin but did not cleave type I collagen over a 12-h period. In the incubation buffer (pH 6.0), 10 µg of the respective substrates was treated with equal volumes of PBS, activated rAc-cathB-1, or activated rAc-cathB-1 plus E64 at 37 °C for 12 h. After incubation, all samples were analyzed on a 5% SDS-PAGE gel followed by Coomassie brilliant blue staining. Molecular weight markers (in kDa) are listed on the side. The substrate used for each experiment is indicated at the top of the gel, and the presence or absence of a recombinant protease or protease inhibitor is indicated at the bottom of each lane. (B) Influence of rAc-cathB-1 on IEC-6 monolayer. IEC-6 cells were grown to confluence and equal amounts of rAc-cathB-1 with or without E64 were applied to cells for 2 h. The blank was made of IEC-6 with PBS added. After incubation, the adherent IEC-6 partly rounded up and the integrity of the cell sheet was disrupted by activated rAc-cathB-1. The cytoplasm and ECM were then labeled with an anti-laminin antibody (green), and the nucleus was stained with DAPI. On the merged images, the dark regions represent the intercellular space. (C) Statistical analysis of the changes to the intercellular space of IEC-6 cells. The dark area was measured and analyzed. The difference between the means for each group of samples was estimated using one-way ANOVA followed by Duncan's multiple comparison test. Asterisk (*), P <0.05; WL, white light; ns: not significant; and bar = 100 µm.

Figure 3 in Angiostrongylus cantonensis cathepsin B-like protease (Ac-cathB-1) is involved in host gut penetration

Figure 3. Activation and pH-dependence profile of rAc-cathB-1. (A) Processing of rAc-cathB-1. Purified rAc-cathB-1 (0.2 mg/mL) was incubated with activation solution or reference solution in a 2:1 (v/v) ratio. Mixtures were incubated at 37 °C for 30 min, and the reaction was stopped by addition of pepstatin A (Sigma-Aldrich) to a final concentration of 1 mM. Samples were analyzed on a 12% SDS-PAGE gel followed by Coomassie brilliant blue staining. MW, molecular weight markers; purified rAc-cathB-1 incubated with activation solution and reference solution as indicated. (B) Enzymatic activity assay. Z-Arg-Arg-7-amido-4-methylcoumarin hydrochloride was used for studying the activity of pepsin-treated rAc-cathB-1 and the control. The fluorescence was measured with excitation and emission wavelengths of 355 and 460 nm, respectively, and data were presented as relative activities, where activity of the control was taken as 1. (C) The pH-dependence profile of activated rAc-cathB-1. The assay was performed with the fluorescent substrate at a final concentration of 50 µM. Fluorescence was measured and data were presented as relative activities of activated rAc-cathB-1, where the highest activity at the pH optimum was taken as 100%. Asterisk (*), P <0.05.