Functional versus compositional tests in the risk assessment of the impacts of pesticides on the soil microbiome DOI Creative Commons
Christopher J. Sweeney,

Melanie Bottoms,

Rishabh Kaushik

et al.

Environmental Toxicology and Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 10, 2025

Abstract The Organisation of Economic Co-operation and Development (OECD) 216 nitrogen transformation test is used to understand the impacts plant protection products (PPPs) on soil microbiome. However, there significant interest in developing European PPP risk assessment include new technologies such as amplicon sequencing assess microbial community composition diversity. We have little understanding how generate endpoints from data sets, their robustness, whether they provide an appropriate level Our study addresses this key knowledge gap. conducted a dose-response OECD with two chemicals, nitrapyrin streptomycin, calculated traditional functional endpoints, accordance guideline, techniques range based bacterial diversity, richness, dissimilarity control, species sensitivity distributions, threshold indicator analysis. show it possible sets; however, these varied significantly calculation method, up 101-fold difference between least most sensitive endpoints. Additionally, relative compared currently metrics was compound dependent, many endpoint methods unable detect microbiome at concentrations deemed ecotoxicologically relevant by 216. shows ecotoxicology did not perform consistently reliably when considering both streptomycin treatments cases enhanced degree over assessments already integrated into assessment.

Language: Английский

Multi-omic approaches for host-microbiome data integration DOI Creative Commons
Ashwin Chetty, Ran Blekhman

Gut Microbes, Journal Year: 2024, Volume and Issue: 16(1)

Published: Jan. 2, 2024

The gut microbiome interacts with the host through complex networks that affect physiology and health outcomes. It is becoming clear these interactions can be measured across many different omics layers, including genome, transcriptome, epigenome, metabolome, proteome, among others. Multi-omic studies of provide insight into mechanisms underlying host-microbe interactions. As more layers are considered, increasingly sophisticated statistical methods required to integrate them. In this review, we an overview approaches currently used characterize multi-omic between data. While a large number have generated deeper understanding host-microbiome interactions, there still need for standardization approaches. Furthermore, would also benefit from collection curation large, publicly available multi-omics datasets.

Language: Английский

Citations

20
Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations DOI Creative Commons
Mark McCauley, Tamar L. Goulet, Colin R. Jackson

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 14, 2023

Abstract Microorganisms play essential roles in the health and resilience of cnidarians. Understanding factors influencing cnidarian microbiomes requires cross study comparisons, yet plethora protocols used hampers dataset integration. We unify 16S rRNA gene sequences from microbiome studies under a single analysis pipeline. reprocess 12,010 samples 186 studies, alongside 3,388 poriferan, 370 seawater samples, 245 cultured Symbiodiniaceae, unifying ~6.5 billion sequence reads. Samples are partitioned by hypervariable region sequencing platform to reduce variability. This systematic review uncovers an incredible diversity 86 archaeal bacterial phyla associated with Cnidaria, highlights key bacteria hosted across host sub-phylum, depth, microhabitat. Shallow (< 30 m) water Alcyonacea Actinaria characterized highly shared relatively abundant microbial communities, unlike Scleractinia most deeper Utilizing V4 region, we find that composition, richness, diversity, structure primarily influenced phylogeny, sampling ocean body, followed microhabitat date. identify geographical generalist specific Endozoicomonas clades within Cnidaria Porifera. forms framework for understanding governing creates baseline assessing stress dysbiosis.

Language: Английский

Citations

23
A robust microbiome signature for autism spectrum disorder across different studies using machine learning DOI Creative Commons
Lucía N. Peralta Marzal, David Rojas-Velázquez,

Douwe Rigters

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Jan. 8, 2024

Abstract Autism spectrum disorder (ASD) is a highly complex neurodevelopmental characterized by deficits in sociability and repetitive behaviour, however there great heterogeneity within other comorbidities that accompany ASD. Recently, gut microbiome has been pointed out as plausible contributing factor for ASD development individuals diagnosed with often suffer from intestinal problems show differentiated microbial composition. Nevertheless, studies rarely agree on the specific bacterial taxa involved this disorder. Regarding potential role of pathophysiology, our aim to investigate whether set relevant classification using sibling-controlled dataset. Additionally, we validate these results across two independent cohorts several confounding factors, such lifestyle, influence both studies. A machine learning approach, recursive ensemble feature selection (REFS), was applied 16S rRNA gene sequencing data 117 subjects (60 cases 57 siblings) identifying 26 discriminate controls. The average area under curve (AUC) bacteria dataset 81.6%. Moreover, selected tenfold cross-validation scheme (a total 223 samples—125 98 controls). We obtained AUCs 74.8% 74%, respectively. Analysis REFS identified can be used predict status children three distinct AUC over 80% best-performing classifiers. Our indicate strong association should not disregarded target therapeutic interventions. Furthermore, work contribute use proposed approach signatures datasets.

Language: Английский

Citations

14
Using New Technologies to Analyze Gut Microbiota and Predict Cancer Risk DOI Creative Commons
Mohammad Amin Hemmati, Marzieh Monemi,

Shima Asli

et al.

Cells, Journal Year: 2024, Volume and Issue: 13(23), P. 1987 - 1987

Published: Dec. 1, 2024

The gut microbiota significantly impacts human health, influencing metabolism, immunological responses, and disease prevention. Dysbiosis, or microbial imbalance, is linked to various diseases, including cancer. It crucial preserve a healthy microbiome since pathogenic bacteria, such as

Language: Английский

Citations

9
The relationship between atmospheric particulate matter, leaf surface microstructure, and the phyllosphere microbial diversity of Ulmus L. DOI Creative Commons

Liren Xu,

Yichao Liu,

Shuxiang Feng

et al.

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: June 17, 2024

Abstract Background Plants can retain atmospheric particulate matter (PM) through their unique foliar microstructures, which has a profound impact on the phyllosphere microbial communities. Yet, underlying mechanisms linking retention by microstructures to variations in communities remain mystery. In this study, we conducted field experiment with ten Ulmus lines. A series of analytical techniques, including scanning electron microscopy, atomic force and high-throughput amplicon sequencing, were applied examine relationship between surface PM retention, diversity L. Results We characterized leaf across Chun exhibited highly undulated abaxial dense stomatal distribution. Langya Xingshan possessed trichomes, while Lieye, Zuiweng, Daguo had sparsely distributed, short trichomes. Duomai, Qingyun, Lang sparse stomata flat surfaces, whereas Jinye distributed but extensive stomata. The mean values for total suspended (TSP), 2.5 , 2.5-10 10-100 > 100 135.76, 6.60, 20.10, 90.98, 13.08 µg·cm − 2 respectively. Trichomes substantially contributed larger undulations enhanced as evidenced positive correlations trichome density adaxial raw microroughness values. Phyllosphere patterns varied among lines, bacteria dominated Sediminibacterium fungi Mycosphaerella Alternaria Cladosporium . Redundancy analysis confirmed that trichomes facilitated capture -associated fungi, less impacted struggled adhere microstructures. Long provided ideal microhabitats retaining PM-borne microbes, feedback loops characteristics, relative abundances microorganisms like Trichoderma Aspergillus Conclusions Based our findings, three-factor network profile was constructed, provides foundation further exploration into how different plants thereby impacting

Language: Английский

Citations

8
Networks as tools for defining emergent properties of microbiomes and their stability DOI Creative Commons

Kacie Kajihara,

Nicole A. Hynson

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: Sept. 28, 2024

Language: Английский

Citations

8
An optimized eDNA protocol for fish tracking in estuarine environments DOI Creative Commons
Fouad El Baidouri, Alison Watts, Jeffrey T. Miller

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 7, 2025

Environmental DNA (eDNA) is revolutionizing how we investigate biodiversity in aquatic and terrestrial environments. It increasingly used for detecting rare invasive species, assessing loss monitoring fish communities, as it considered a cost-effective noninvasive approach. Some environments, however, can be challenging eDNA analyses. Estuarine systems are highly productive, complex but samples collected from these settings may exhibit PCR inhibition low read recovery. Here present an approach turbid, productive estuarine systems. The workflow includes bead-based extraction, removal, high fidelity specificity polymerase (Platinum SuperFi II) multiplexing the universal MiFish primers. By applying this hybrid method to variety of with known inhibition, have more than doubled number recovered species while removing most off-target amplification.

Language: Английский

Citations

1
The respiratory microbiota alpha-diversity in chronic lung diseases: first systematic review and meta-analysis DOI Creative Commons

Marta Avalos-Fernandez,

Thibaud Alin,

Clémence Métayer

et al.

Respiratory Research, Journal Year: 2022, Volume and Issue: 23(1)

Published: Aug. 23, 2022

Abstract Background While there seems to be a consensus that decrease in gut microbiome diversity is related decline health status, the associations between respiratory and chronic lung disease remain matter of debate. We provide systematic review meta-analysis studies examining microbiota alpha-diversity patients with asthma, obstructive pulmonary (COPD), cystic fibrosis (CF) or bronchiectasis (NCFB), which control group based on status healthy subjects provided for comparison. Results reviewed 351 articles title abstract, 27 met our inclusion criteria review. Data from 24 these were used meta-analysis. observed trend CF have less diverse than individuals. However, substantial heterogeneity was present detailed using random-effects models, limits comparison studies. Conclusions Knowledge under construction, moment, it measurements are not enough documented fully understand link health, excepted context represents most studied consistent published data function. Whether differences profiles an impact symptoms and/or evolution deserves further exploration.

Language: Английский

Citations

37
A next-generation sequencing approach for the detection of mixed species in canned tuna DOI Creative Commons

Regina Klapper,

Amaya Velasco,

Maik Döring

et al.

Food Chemistry X, Journal Year: 2023, Volume and Issue: 17, P. 100560 - 100560

Published: Jan. 5, 2023

Tuna cans are relevant seafood products for which mixtures of different tuna species not allowed according to European regulations. In order support the prevention food fraud and mislabelling, a next-generation sequencing methodology based on mitochondrial cytochrome b control region markers has been tested. Analyses defined DNA, fresh tissue canned revealed qualitative and, some extent, semiquantitative identification species. While choice bioinformatic pipeline had no influence in results (p = 0.71), quantitative differences occurred depending treatment sample, marker, species, mixture < 0.01). The that matrix-specific calibrators or normalization models should also be used NGS. method represents an important step towards routine this analytically challenging matrix. Tests commercial samples uncovered mixed cans, being compliance with EU

Language: Английский

Citations

17
Microbiota Ecosystem Services in Vineyards and Wine: A Review DOI Creative Commons
Isabel García-Izquierdo, Víctor J. Colino-Rabanal, Mercedes Tamame

et al.

Agronomy, Journal Year: 2024, Volume and Issue: 14(1), P. 131 - 131

Published: Jan. 4, 2024

The domestication of vines started in Asia 11,000 years ago, although it was not until the 19th century that oenology established as a scientific discipline thanks to research Louis Pasteur on role microorganisms wine fermentation. At present time, progression next-generation sequencing (NGS) technologies is helping facilitate identification microbial dynamics during winemaking. These advancements have aided winemakers gaining more comprehensive understanding microbiota fermentation process, which, turn, ultimately responsible for delivery provisioning (wine features and its production), regulating (such carbon storage by vineyards, regulation soil quality, biocontrol pests diseases) or cultural aesthetic values vineyard landscapes, scholarly enjoyment wine, sense belonging wine-growing regions) ecosystem services. To our knowledge, this first review state knowledge services sector, well possibility valuing them monetary terms operating logic chains, such those suggested SEEA-EA framework. This paper concludes with management practices may enhance value smart farming task.

Language: Английский

Citations

7