Fifty important research questions in microbial ecology

FEMS Microbiology Ecology, Год журнала: 2017, Номер 93(5)

Опубликована: Март 31, 2017

Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. can now be investigated in unprecedented detail, although there is still a wealth open questions to tackled. Here we identify 50 research fundamental importance science or application ecology, with intention summarising field bringing focus new avenues. Questions are categorised seven themes: host-microbiome interactions; health infectious diseases; human food security; changing world; environmental processes; functional diversity; processes. Many recognise that microbes provide an extraordinary array diversity harnessed solve real-world problems. Our limited knowledge spatial temporal variation function also reflected, as need integrate micro- macro-ecological concepts, derived from studies humans other diverse organisms. Although not exhaustive, presented intended stimulate discussion for researchers, funders policy makers, informing future agenda ecology.

Язык: Английский

---

High-order interactions distort the functional landscape of microbial consortia

PLoS Biology, Год журнала: 2019, Номер 17(12), С. e3000550 - e3000550

Опубликована: Дек. 12, 2019

Understanding the link between community composition and function is a major challenge in microbial population biology, with implications for management of natural microbiomes design synthetic consortia. Specifically, it poorly understood whether functions can be quantitatively predicted from traits species monoculture. Inspired by study complex genetic interactions, we have examined how amylolytic rate combinatorial assemblages six starch-degrading soil bacteria depend on separate functional contributions each their interactions. Filtering our results through theory biochemical kinetics, show that this simple additive absence interactions among members. For about half combinatorially assembled consortia, dominated pairwise higher-order other half, despite presence strong competitive We explain mechanistic basis these findings propose quantitative framework allows us to effect behavioral dynamics Our suggest robustness consortium critically affects ability predict bottom-up engineer ecosystem communities.

Язык: Английский

---

ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies

Briefings in Bioinformatics, Год журнала: 2018, Номер 21(2), С. 621 - 636

Опубликована: Дек. 7, 2018

Label-free quantification (LFQ) with a specific and sequentially integrated workflow of acquisition technique, tool processing method has emerged as the popular technique employed in metaproteomic research to provide comprehensive landscape adaptive response microbes external stimuli their interactions other organisms or host cells. The performance LFQ is highly dependent on studied data. Hence, it essential discover most appropriate one for data set. However, challenging perform such discovery due large number possible workflows multifaceted nature evaluation criteria. Herein, web server ANPELA (https://idrblab.org/anpela/) was developed validated first enabling assessment whole (collective by five well-established criteria distinct underlying theories), enabled identification optimal workflow(s) ranking. not only automatically detects diverse formats generated all tools but also provides complete set methods among available servers stand-alone tools. Systematic validation using benchmarks revealed ANPELA's capabilities 1 discovering well-performing workflow(s), (2) from multiple perspectives (3) validating accuracy spiked proteins. unique ability evaluate enables LFQs ranking 560 workflows. Therefore, great potential applications studies requiring techniques, many features are shared proteomic studies.

Язык: Английский

---

Emerging Priorities for Microbiome Research

Frontiers in Microbiology, Год журнала: 2020, Номер 11

Опубликована: Фев. 19, 2020

Microbiome research has increased dramatically in recent years, driven by advances technology and significant reductions the cost of analysis. Such unlocked a wealth data, which yielded tremendous insight into nature microbial communities, including their interactions effects, both within host an external environment as part ecological community. Understanding role microbiota, dynamic with hosts other microbes, can enable engineering new diagnostic techniques interventional strategies that be used diverse spectrum fields, spanning from ecology agriculture to medicine forensics exobiology. From June 19-23 2017, NIH NSF jointly held Innovation Lab on Quantitative Approaches Biomedical Data Science Challenges our Microbiome. This review is inspired some topics arose priority areas this unique, interactive workshop. The goal summarize Lab's findings introducing reader emerging challenges, exciting potential, current directions microbiome research. broken five key topic areas: (1) between microbes human body, (2) evolution played microbe-microbe interactions, (3) analytical mathematical methods currently research, (4) leveraging knowledge composition develop solutions, (5) approaches may enabled selectively altering composition. As such, seeks arm broad understanding priorities challenges today provide inspiration for future investigation multi-disciplinary collaboration.

Язык: Английский

---

Microbiome diversity protects against pathogens by nutrient blocking

Science, Год журнала: 2023, Номер 382(6676)

Опубликована: Дек. 14, 2023

The human gut microbiome plays an important role in resisting colonization of the host by pathogens, but we lack ability to predict which communities will be protective. We studied how bacteria influence two major bacterial both vitro and gnotobiotic mice. Whereas single species alone had negligible effects, resistance greatly increased with community diversity. Moreover, this community-level rested critically upon certain being present. explained these ecological patterns through collective resistant consume nutrients that overlap those used pathogen. Furthermore, applied our findings successfully resist a novel target strain. Our work provides reason why diversity is beneficial suggests route for rational design pathogen-resistant communities.

Язык: Английский

---