Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles

Nature Neuroscience, Journal Year: 2023, Volume and Issue: 26(7), P. 1208 - 1217

Published: June 26, 2023

Autism spectrum disorder (ASD) is a neurodevelopmental characterized by heterogeneous cognitive, behavioral and communication impairments. Disruption of the gut-brain axis (GBA) has been implicated in ASD although with limited reproducibility across studies. In this study, we developed Bayesian differential ranking algorithm to identify ASD-associated molecular taxa profiles 10 cross-sectional microbiome datasets 15 other datasets, including dietary patterns, metabolomics, cytokine human brain gene expression profiles. We found functional architecture along GBA that correlates heterogeneity phenotypes, it amino acid, carbohydrate lipid predominantly encoded microbial species genera Prevotella, Bifidobacterium, Desulfovibrio Bacteroides changes, restrictive patterns pro-inflammatory The revealed age-matched sex-matched cohorts not present sibling-matched cohorts. also show strong association between temporal changes composition phenotypes. summary, propose framework leverage multi-omic from well-defined investigate how influences ASD.

Language: Английский

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Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies

Journal of Animal Science, Journal Year: 2022, Volume and Issue: 100(2)

Published: Feb. 1, 2022

Abstract Microbiome studies in animal science using 16S rRNA gene sequencing have become increasingly common recent years as costs continue to fall and bioinformatic tools more powerful user-friendly. The combination of molecular biology, microbiology, microbial ecology, computer science, bioinformatics—in addition the traditional considerations when conducting an study—makes microbiome sometimes intimidating due intersection different fields. objective this review is serve a jumping-off point for those scientists less familiar with analyses bring up issues concerns that arise planning study from design through analysis. This includes overview sequencing, its advantages, limitations; experimental such design, sample size, pooling, locations; wet lab field handing, cell lysis, low biomass samples, library preparation, controls; computational identification contamination, accounting uneven depth, constructing diversity metrics, assigning taxonomy, differential abundance testing, and, finally, data availability. In general considerations, we highlight some special by species type.

Language: Английский

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Hydrodynamic and anthropogenic disturbances co-shape microbiota rhythmicity and community assembly within intertidal groundwater-surface water continuum

Water Research, Journal Year: 2023, Volume and Issue: 242, P. 120236 - 120236

Published: June 16, 2023

Language: Английский

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Sea ice presence is linked to higher carbon export and vertical microbial connectivity in the Eurasian Arctic Ocean

Communications Biology, Journal Year: 2021, Volume and Issue: 4(1)

Published: Nov. 3, 2021

Arctic Ocean sea ice cover is shrinking due to warming. Long-term sediment trap data shows higher export efficiency of particulate organic carbon in regions with seasonal compared without ice. To investigate this sea-ice enhanced export, we how different early summer phytoplankton communities seasonally ice-free and ice-covered the Fram Strait affect vertical dispersal microbes. In situ collected aggregates revealed two-fold diatom-rich regions, Phaeocystis region. Using microbial source tracking, found that were also associated more surface-born clades exported deep sea. Taken together, our results showed are responsible for high provide strong connectivity. Therefore, continuous loss may decrease efficiency, thus pelagic-benthic coupling, potential repercussions deep-sea ecosystems.

Language: Английский

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Current Applications of Absolute Bacterial Quantification in Microbiome Studies and Decision-Making Regarding Different Biological Questions

Microorganisms, Journal Year: 2021, Volume and Issue: 9(9), P. 1797 - 1797

Published: Aug. 24, 2021

High throughput sequencing has emerged as one of the most important techniques for characterizing microbial dynamics and revealing bacteria host interactions. However, data interpretation using this technique is mainly based on relative abundance ignores total load. In certain cases, absolute more than compositional data, microbiota solely can be misleading. The available approaches quantification are highly diverse challenging, especially in differing biological situations, such distinguishing between live dead cells, specific taxa, enumeration low biomass samples, large sample size feasibility, detection various other cellular features. review, we first illustrate importance integrating into microbiome interpretation. Second, briefly discuss widely used cell-based molecular-based bacterial load methods, including fluorescence spectroscopy, flow cytometry, 16S qPCR, qRT-PCR, ddPCR, reference spike-in. Last, present a decision-making scheme methods different questions some latest quantitative procedure modifications.

Language: Английский

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Microbiome Analysis via OTU and ASV-Based Pipelines—A Comparative Interpretation of Ecological Data in WWTP Systems

Bioengineering, Journal Year: 2022, Volume and Issue: 9(4), P. 146 - 146

Published: March 29, 2022

Linking community composition and ecosystem function via the cultivation-independent analysis of marker genes, e.g., 16S rRNA gene, is a staple microbial ecology dependent disciplines. The certainty results, independent bioinformatic handling, imperative for any advances made within field. In this work, thermophilic anaerobic co-digestion experimental data, together with primary waste-activated sludge prokaryotic were analyzed two pipelines that apply different principles when dealing technical, sequencing, PCR biases. One pipeline (VSEARCH) employs clustering methods, generating individual operational taxonomic units (OTUs), while other (DADA2) based on sequencing error correction algorithms generates exact amplicon sequence variants (ASVs). outcomes both compared framework ecological-driven data analysis. Both provided comparable results would generally allow same interpretations. Yet, approaches also delivered compositions differed between 6.75% 10.81% pipelines. Inconsistencies observed linked to biologically driven variability in samples, which affected differently. These pipeline-dependent differences assignment could lead conclusions interfere downstream such mis- or not-identified species, network predictions their respective service.

Language: Английский

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SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(26)

Published: June 21, 2022

One of the biggest challenges in microbiome research environmental and medical samples is to better understand functional properties microbial community members at a single-cell level. Single-cell isotope probing has become key tool for this purpose, but current detection methods determination incorporation into single cells do not allow high-throughput analyses. Here, we report on development an imaging-based approach termed stimulated Raman scattering-two-photon fluorescence situ hybridization (SRS-FISH) metabolism identity analyses communities with resolution. SRS-FISH offers imaging speed 10 100 ms per cell, which two three orders magnitude faster than achievable by state-of-the-art methods. Using technique, delineated metabolic responses 30,000 individual various mucosal sugars human gut via deuterium from heavy water as activity marker. Application investigate utilization host-derived nutrients major taxa revealed that response tends be dominated Bacteroidales, unexpected finding Clostridia can outperform Bacteroidales foraging fucose. With high sensitivity speed, will enable researchers probe fine-scale temporal, spatial, patterns complex unprecedented detail.

Language: Английский

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Comparative Analysis of Primers Used for 16S rRNA Gene Sequencing in Oral Microbiome Studies

Methods and Protocols, Journal Year: 2023, Volume and Issue: 6(4), P. 71 - 71

Published: Aug. 6, 2023

Recent advances in genomic technologies have enabled more in-depth study of the oral microbiome. In this study, we compared amplicons generated by primers targeting different sites 16S rRNA gene found Human Oral Microbiome Database (HOMD). Six sets primer V1-V2, V1-V3, V3-V4, V4-V5, V5-V7 and V6-V8 regions were tested via silico simulation. Primers V4-V5 than 90% original input sequences. V1-V2 V1-V3 exhibited a low number mismatches unclassified sequences at taxonomic level, but there notable discrepancies species level. Phylogenetic tree comparisons showed V3-V4 performances similar to whole 16s RNA region terms separating total microbiomes periodontopathogens. an analysis clinical samples, superior performance for identifying taxa had better resolution sensitivity Streptococcus primers. conclusion, best microbiome studies. addition, demonstrates need careful PCR selections.

Language: Английский

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Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(10), P. 1612 - 1625

Published: July 8, 2023

The Arctic Ocean is experiencing unprecedented changes because of climate warming, necessitating detailed analyses on the ecology and dynamics biological communities to understand current future ecosystem shifts. Here, we generated a four-year, high-resolution amplicon dataset along with one annual cycle PacBio HiFi read metagenomes from East Greenland Current (EGC), combined this datasets spanning different spatiotemporal scales (Tara MOSAiC) assess impact Atlantic water influx sea-ice cover bacterial in Ocean. Densely ice-covered polar waters harboured temporally stable, resident microbiome. reduced resulted dominance seasonally fluctuating populations, resembling process "replacement" through advection, mixing environmental sorting. We identified signature populations distinct regimes, including night high-ice cover, assessed their ecological roles. Dynamics were consistent across wider Arctic; e.g. those associated dense ice winter EGC abundant central winter. Population- community-level revealed metabolic distinctions between bacteria affiliated conditions; former increased potential use bacterial- terrestrial-derived substrates or inorganic compounds. Our evidence over provides novel insights into indicates progressing Biological Atlantification warming Ocean, consequences for food webs biogeochemical cycles.

Language: Английский

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Roadmap for the integration of environmental microbiomes in risk assessments under EFSA's remit

EFSA Supporting Publications, Journal Year: 2024, Volume and Issue: 21(2)

Published: Feb. 1, 2024

Scientific interest in the use of environmental microbiomes for risk assessment is rapidly growing, as exemplified by various EFSA opinions. In absence official regulatory guidelines on how to integrate assessment, aims this report are therefore determine whether microbiome studies can be used such purposes, and propose a roadmap integration assessments under EFSA's remit. The identifies current gaps (in terms knowledge from technical point view) barriers that might delay implementation methods, offers recommendations standardised (multi-)omics techniques purposes. Our main findings identified five priorities: (i) defining core (what it encompasses what made of, including identification bioindicators) assess impact any type disturbance; (ii) standardising methodologies protocols, sampling interpretation, guarantee comparability analyses; (iii) developing tools facilitate interpretation; (iv) collecting microbiome-based data shared, curated maintained databases; (v) setting up European Network Microbiome Laboratories reach an agreement standardise studies, interactions between researchers access or samples, actively include multiple stakeholders discussions involving assessment. There both short- longer-term priorities, all which highlight need mobilise concurrently different agencies institutions, well research. also points out capacity building training, acceptance emerging technology, communication issues. These will hopefully contribute elaboration widely accepted framework dealing with.

Language: Английский

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