{"id":1131,"date":"2020-11-02T15:49:31","date_gmt":"2020-11-02T15:49:31","guid":{"rendered":"https:\/\/website.prod.unilu.spikeseed.cloud\/fr\/news\/understanding-the-factors-that-shape-microbiomes\/"},"modified":"2020-11-02T15:49:31","modified_gmt":"2020-11-02T15:49:31","slug":"understanding-the-factors-that-shape-microbiomes","status":"publish","type":"news","link":"https:\/\/www.uni.lu\/fr\/news\/understanding-the-factors-that-shape-microbiomes\/","title":{"rendered":"Understanding the factors that shape microbiomes"},"content":{"rendered":"

In two scientific articles recently published in high-impact journals \u2013 Nature Microbiology and Nature Communications \u2013 the Systems Ecology group at the University of Luxembourg’s Luxembourg Centre for Systems Biomedicine (LCSB) led by Prof. Paul Wilmes studied the dynamics of microbial communities (microbiomes) over several microbial generations. Their results provide a better understanding of the microorganisms that live in biological wastewater treatment plants, with potential impact on the performance of one of the most widely used biotechnological process on our planet. Using this model system, their work also offers new insights into the many factors, both abiotic and biotic, that shape microbiomes. The fundamental knowledge acquired during these studies will help to predict dynamics and ultimately control microbial communities of interest, including the human microbiome.<\/p>\n

\nThe roles of viruses, plasmids and CRISPR-immunity<\/h3>\n

The dynamics of microbiomes \u2013 such as those found in a biological wastewater treatment plants \u2013 are driven by both environmental and biological factors. Among the biological factors are bacteriophages and plasmids: invasive mobile genetic elements (iMGEs) which move between organisms and can transfer detrimental or beneficial genetic material to their hosts.<\/p>

The researchers of the University of Luxembourg studied the impact of viruses (bacteriophages) and plasmids on a model microbial community in a wastewater treatment plant by collecting samples over one and a half years. They especially focused on one bacterial immune system: a defence mechanism used by microorganisms against invasion by iMGEs. Through this so-called CRISPR-Cas system (nowadays widely used as a genetic engineering tool), bacteria can recognise foreign elements and integrate parts of the mobile genetic material into their own genomes. The integrated sequences serve as a genetic memory bank and can be used to interfere with future invasions. By elucidating the CRISPR-mediated interactions between the microorganisms and both bacteriophages and plasmids, the scientists were able to understand better how the structure of the microbial community is shaped by these iMGEs.<\/p>

The Nature Microbiolog<\/i> showed that plasmids are highly abundant within the community and have a strong impact on its dynamics. The results suggest that plasmids are the main target of the CRISPR systems, allowing bacteria to selectively retain potentially beneficial genetic material, for example antimicrobial resistance genes. \u201cThis is entirely new as it was previously thought that the viruses were targeted predominantly,\u201d explains Susana Mart\u00ednez Arbas<\/a>, PhD student at the LCSB and first author of the paper. \u201cIt is an important finding as these interactions play a key role in promoting adaptation and diversity within microbiomes. The dynamics are also essential to understand the spread of antimicrobial resistance genes which are typically encoded by plasmids.\u201dy<\/i><\/p>

Understanding the factors impacting microbial populations is crucial as it can help to both devise measures against deleterious species and predict how the community will evolve over time. Based on the researcher\u2019s observations, iMGEs and CRISPR-based interactions should now be taken into account as their incorporation can provide more comprehensive models of community dynamics. \u201cThis can of course be used to improve the performance of wastewater treatment plants, but it could also be key in maintaining a healthy gut microbiome for example,\u201d concludes Susana Mart\u00ednez Arbas.<\/p>

\n \n\"\"\n

\n Wastewater Treatment Plant \u00a9scienceRELATIONS <\/p>\n <\/figure>\n

\nMicrobiomes\u2019 responses to perturbations<\/h3>\n

To allow long-term stable operation of biotechnological processes such as wastewater treatment plants or to maintain the balance of the human microbiome, it is also important to understand how microbial ecosystems respond to disturbances. This was at the heart of the Nature Communications<\/i>. The researchers specifically studied resistance and resilience within the microbial community, especially focusing on lipid-accumulating populations as these bacteria have a competitive advantage in fluctuating environments and have compelling potential to be used in circular economic models.<\/p>

First, they identified all the ecological niches present in the wastewater treatment plant ecosystem (a niche is the match of a species to a specific environmental condition). Then they showed how, under constant conditions, the complementarity of the microorganisms occupying these different niches, as well as the interspecific competition for certain resources, guarantees the stability of the ecosystem and thus of the biotechnological process.<\/p>

Their results also highlighted that in case of perturbation, such as a change in the availability of nutrients, the composition of the community shifts temporarily: some microorganisms are able to quickly adapt to variations in the environment by adopting specific strategies. For example, one microbial species exhibits extensive plasticity in gene expression, meaning that a set of genes within a species can produce more than one phenotype when exposed to different conditions. The ability to adjust their phenotype \u2013 the sum of the organism traits \u2013 allows the population to be resistant to fluctuations.<\/p>

\u201cGlobally, the study shows that this microbiome\u2019s resistance and resilience \u2013 its capacity to recover after a disturbance \u2013 are a function of phenotypic plasticity and niche complementarity,\u201d describes Dr Malte Herold, first author of the article and former PhD student within the Systems Ecology group. \u201cEven though a biological wastewater treatment plant is a controlled process, some factors fluctuate. It has an impact on microbial dynamics and then on the process\u2019 efficiency. So, our results are particularly relevant for the development of future ecological engineering efforts and to achieve our linked sustainability goals,\u201d Dr Herold points out.<\/p>\n

\nHarnessing integrated meta-omics\u2026<\/h3>\n

On top of providing new insights into the works of microbial ecosystems, the two publications also highlight the potential of integrated meta-omics approaches to study microbiomes. In both studies, they allowed the researchers to identify ecological niches, characterise microbial activity, track gene expression and get an in-depth understanding of the interactions that shape the community\u2019s structure.<\/p>

\u201cThese articles showcase the expertise acquired by the Systems Ecology group over the years. Our team is now developing new methods in this emerging field, with applications far beyond wastewater treatment,\u201d emphasises Prof. Paul Wilmes. \u201cThese two studies set the scene for many new exciting applications, including in the context of engineering the human microbiome.\u201d<\/p>\n

\n\u2026 and interdisciplinary collaboration within the university\u00a0<\/h3>\n

These studies have been possible thanks to University of Luxembourg collaborations coordinated by the Systems Ecology group<\/a> at the LCSB and the Department of Life Sciences and Medicine<\/a> (DLSM) of the Faculty of Science, Technology and Medicine (FSTM). \u201cOur group is delighted to form an interdisciplinary bridge between the LCSB, DLSM and FSTM\u201d, underlines Prof. Paul Wilmes<\/a>.<\/p>

<\/p>\n

\nReferences:<\/h5>\n

Nat Microbio<\/i><\/p>

Nat Commun<\/i><\/p>

<\/p>\n

\nInternational collaboration partners:<\/h5>\n

– MetaGenoPolis, INRAE, Universit\u00e9 Paris-Saclay, France <\/p>

– Singapore Centre for Environmental Life Sciences Engineering, Singapore<\/p>

– The Translational Genomics Research Institute, USA<\/p>

– Institute for Systems Biology, USA <\/p>

– School of Informatics,Computing and Engineering, Indiana University, USA <\/p>

– German Centre for Integrative Biodiversity Research, Germany <\/p>

– \u00c9quipe Adaptations et Interactions Microbiennes, Universit\u00e9 de Strasbourg, CNRS, France<\/p>

– Laboratory of Molecular Bacteriology, KU Leuven, Belgium<\/p>

– Harvard T.H. Chan School of Public Health, Harvard University, USA<\/p><\/div><\/section>","protected":false},"excerpt":{"rendered":"

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The fundamental knowledge acquired during these studies will help to predict dynamics and ultimately control microbial communities of interest, including the human microbiome.<\/p>\n","protected":false},"author":0,"featured_media":0,"template":"","format":"standard","meta":{"featured_image_focal_point":[],"show_featured_caption":false,"ulux_newsletter_groups":"","uluxPostTitle":"","uluxPrePostTitle":"","_trash_the_other_posts":false,"_price":"","_stock":"","_tribe_ticket_header":"","_tribe_default_ticket_provider":"","_tribe_ticket_capacity":"0","_ticket_start_date":"","_ticket_end_date":"","_tribe_ticket_show_description":"","_tribe_ticket_show_not_going":false,"_tribe_ticket_use_global_stock":"","_tribe_ticket_global_stock_level":"","_global_stock_mode":"","_global_stock_cap":"","_tribe_rsvp_for_event":"","_tribe_ticket_going_count":"","_tribe_ticket_not_going_count":"","_tribe_tickets_list":"[]","_tribe_ticket_has_attendee_info_fields":false},"news-category":[3],"news-topic":[19],"organisation":[25,202,226],"authorship":[],"acf":[],"yoast_head":"\nUnderstanding the factors that shape microbiomes - Universit\u00e9 du Luxembourg<\/title>\n<meta name=\"description\" content=\"In two scientific articles recently published in high-impact journals \u2013 Nature Microbiology and Nature Communications \u2013 the Systems Ecology group at the University of Luxembourg's Luxembourg Centre for Systems Biomedicine (LCSB) led by Prof. Paul Wilmes studied the dynamics of microbial communities (microbiomes) over several microbial generations. 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