Effects of Tree Composition and Soil Depth on Structure and Functionality of Belowground Microbial Communities in Temperate European Forests DOI Creative Commons
Luis Daniel Prada‐Salcedo,

Juan Pablo Prada-Salcedo,

Anna Heintz‐Buschart

et al.

Frontiers in Microbiology, Journal Year: 2022, Volume and Issue: 13

Published: July 11, 2022

Depending on their tree species composition, forests recruit different soil microbial communities. Likewise, the vertical nutrient gradient along profiles impacts these communities and activities. In forest soils, bacteria fungi commonly compete, coexist, interact, which is challenging for understanding complex mechanisms behind structuring. Using amplicon sequencing, we analyzed bacterial fungal diversity in relation to composition depth. Moreover, employing random models, identified indicator taxa of plots composed either deciduous or evergreen trees, mixtures, as well three depths. We expected that depth affect community structure differently. Indeed, relative abundances changed more across depths than composition. The Shannon was particularly affected by proportion trees. Our results also reflected are primarily shaped depth, while were influenced An increasing trees did not provoke differences main metabolic functions, e.g., carbon fixation, degradation, photosynthesis. However, significant responses related specialized metabolisms detected. Saprotrophic, arbuscular mycorrhizal, plant pathogenic topsoil. Prominent characterized be r-strategists, whereas K-strategists dominated plots. Considering simultaneously unravel communities, pathways functional guilds have potential enlighten maintain functionality provide resistance against disturbances.

Language: Английский

Gut microbiome, big data and machine learning to promote precision medicine for cancer DOI
Giovanni Cammarota, Gianluca Ianiro,

Anna M. Ahern

et al.

Nature Reviews Gastroenterology & Hepatology, Journal Year: 2020, Volume and Issue: 17(10), P. 635 - 648

Published: July 9, 2020

Language: Английский

Citations

242
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses DOI Creative Commons
Ana Elena Pérez‐Cobas, Laura Gomez‐Valero, Carmen Buchrieser

et al.

Microbial Genomics, Journal Year: 2020, Volume and Issue: 6(8)

Published: July 24, 2020

Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. is a culture-independent method that allows identification characterization organisms from all kinds samples. Whole-genome shotgun analyses total DNA chosen sample to determine presence micro-organisms domains life their genomic content. Importantly, whole-genome approach reveals diversity present, but can also give insights into functional potential identified. The based on specific region. It one describe composition taxonomic groups present in sample. frequently used analyse biodiversity ecosystems. Despite its importance, analysis metagenomic data quite challenge. Here we review primary workflows software for both approaches discuss current challenges field.

Language: Английский

Citations

198
Machine learning applications in microbial ecology, human microbiome studies, and environmental monitoring DOI Creative Commons
Ryan B. Ghannam, Stephen M. Techtmann

Computational and Structural Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19, P. 1092 - 1107

Published: Jan. 1, 2021

Advances in nucleic acid sequencing technology have enabled expansion of our ability to profile microbial diversity. These large datasets taxonomic and functional diversity are key better understanding ecology. Machine learning has proven be a useful approach for analyzing community data making predictions about outcomes including human environmental health. applied profiles been used predict disease states health, quality presence contamination the environment, as trace evidence forensics. appeal powerful tool that can provide deep insights into communities identify patterns data. However, often machine models black boxes specific outcome, with little how arrived at predictions. Complex algorithms may value higher accuracy performance sacrifice interpretability. In order leverage more translational research related microbiome strengthen extract meaningful biological information, it is important interpretable. Here we review current trends applications ecology well some challenges opportunities broad application communities.

Language: Английский

Citations

181
Applying artificial neural networks (ANNs) to solve solid waste-related issues: A critical review DOI
Ankun Xu, Huimin Chang, Yingjie Xu

et al.

Waste Management, Journal Year: 2021, Volume and Issue: 124, P. 385 - 402

Published: March 2, 2021

Language: Английский

Citations

146
Predicting measures of soil health using the microbiome and supervised machine learning DOI Creative Commons
Roland C. Wilhelm, Harold M. van Es, Daniel H. Buckley

et al.

Soil Biology and Biochemistry, Journal Year: 2021, Volume and Issue: 164, P. 108472 - 108472

Published: Oct. 29, 2021

Language: Английский

Citations

110
Global epistasis and the emergence of function in microbial consortia DOI Creative Commons
Juan Díaz‐Colunga,

Abigail Skwara,

Jean C. C. Vila

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(12), P. 3108 - 3119.e30

Published: May 21, 2024

The many functions of microbial communities emerge from a complex web interactions between organisms and their environment. This poses significant obstacle to engineering consortia, hindering our ability harness the potential microorganisms for biotechnological applications. In this study, we demonstrate that collective effect ecological microbes in community can be captured by simple statistical models predict how adding new species will affect its function. These predictive mirror patterns global epistasis reported genetics, they quantitatively interpreted terms pairwise members. Our results illuminate an unexplored path predicting function consortia composition, paving way optimizing desirable properties bringing tasks biological at genetic, organismal, scales under same quantitative formalism.

Language: Английский

Citations

20
Mechanistic insights into the attenuation of intestinal inflammation and modulation of the gut microbiome by krill oil using in vitro and in vivo models DOI Creative Commons
Fang Liu, Allen Smith, Gloria Solano‐Aguilar

et al.

Microbiome, Journal Year: 2020, Volume and Issue: 8(1)

Published: June 4, 2020

The anti-inflammatory property of ω-3 polyunsaturated fatty acids (PUFA) has been exploited in the management inflammatory bowel disease (IBD) with promising results. However, it remains unclear if PUFA play a significant role resolution inflammation and promotion mucosal healing. Krill oil (KO) is natural product rich potent antioxidant, astaxanthin. In this study, we attempted to understand mechanisms through which KO modulates gut microbiome metabolome using vitro vivo colitis models multi-omics based approach.KO significantly decreased LPS-induced IL1β TNFα expression human macrophages dose-dependent manner by regulating broad spectrum signaling pathways, including NF-κB NOD-like receptor signaling, displayed synergistic effect COX2 IKK2 inhibitors attenuating pathways. Moreover, was involved promoting M2 polarization enhancing macrophage-mediated intracellular bacterial killing. Parasite-dependent intestinal damage microbial dysbiosis induced Trichuris suis infection pigs were partially restored feeding KO. supplementation reduced abundance Rickettsiales several species Lactobacillus, among important features identified random forests analysis contributing classification accuracy for supplementation. Several signatures strong predictive power status both identified. inhibitory on histidine metabolism untargeted metabolomics. key metabolites related histamine suppressing gene encoding L-histidine decarboxylase colon mucosa reducing biosynthesis origin. pro-resolving properties validated Citrobacter rodentium-induced Th1-dependent murine model. Further, high prediction colitis-related pathophysiological traits mice.The findings from study provided mechanistic basis optimizing microbiome-inspired alternative therapeutics IBD. identified, particularly those phenotypes, will facilitate development biomarkers associated appropriate dietary intervention manage inflammation. Video abstract.

Language: Английский

Citations

99
Fermented food products in the era of globalization: tradition meets biotechnology innovations DOI
Andrea Galimberti, Antonia Bruno, Giulia Agostinetto

et al.

Current Opinion in Biotechnology, Journal Year: 2020, Volume and Issue: 70, P. 36 - 41

Published: Nov. 21, 2020

Language: Английский

Citations

88
Next generation microbiome applications for crop production — limitations and the need of knowledge-based solutions DOI
Birgit Mitter, Günter Brader,

Nikolaus Pfaffenbichler

et al.

Current Opinion in Microbiology, Journal Year: 2019, Volume and Issue: 49, P. 59 - 65

Published: June 1, 2019

Language: Английский

Citations

85
Machine learning methods for microbiome studies DOI
Junghyun Namkung

The Journal of Microbiology, Journal Year: 2020, Volume and Issue: 58(3), P. 206 - 216

Published: Feb. 27, 2020

Language: Английский

Citations

85