Cooperation is key to success in microbial communities

jg533 — Mon, 04 Jan 2021 16:15:20 +0000

̽��ֱ��results are published today in the journal Nature Microbiology.

̽��ֱ��study used kefir as a model to study metabolic interactions within microbial communities. It is easy to grow, and consists of around 40 different species - providing a ‘Goldilocks zone’ of complexity that is not too small yet not too unwieldy to study in detail. Kefir is composed of ‘grains’ - resembling small pieces of cauliflower - that have fermented in milk to produce a probiotic drink composed of bacteria and yeasts.

̽��ֱ��researchers were surprised to discover that the dominant species of Lactobacillus bacteria found in kefir grains cannot survive on their own in milk. However, the different species work together, feeding on each other’s metabolites in the kefir culture to support each other.

“ ̽��ֱ��kefir grain acts as a ‘base camp’ for the kefir community, from which microbes colonise the milk in a complex, yet organised and cooperative manner,” said Dr Kiran Patil, Director of Research at the ̽��ֱ�� of Cambridge’s MRC Toxicology Unit, group leader at EMBL, and senior author of the study.

̽��ֱ��researchers combined a variety of state-of-the-art methods including metabolomics (studying metabolites’ chemical processes), transcriptomics (studying the genome-produced RNA transcripts), and mathematical modelling. This revealed not only key molecular interaction agents like amino acids, but also the contrasting species dynamics between the grains and the milk.

While scientists know that microorganisms often live in communities and depend on their fellow community members for survival, there was previously very little understanding of how this works. Lab models have historically been limited to two or three different microbial species.

“Kefir microbial communities have many member species, with individual growth patterns that adapt to their current environment. This means fast- and slow-growing species and some that alter their speed according to nutrient availability,” said Sonja Blasche, a postdoc in the Patil group at EMBL and joint first author of the paper.

Kefir is one of the world’s oldest fermented foods and has many purported health benefits, including improving digestion and lowering blood pressure and blood glucose levels.

This phenomenon of microbial cooperation is not limited to kefir. In another paper from Patil’s group, published today in the journal Nature Ecology and Evolution, scientists combined data from thousands of microbial communities across the globe - from soil to the human gut - to understand similar cooperative relationships.

Advanced metabolic modelling showed that the co-occurring groups of bacteria are either highly competitive or highly cooperative. This stark polarisation has not been observed before and sheds light on evolutionary processes that shape microbial ecosystems. While both competitive and cooperative communities are prevalent, the cooperators seem to be more successful: they are more abundant and occupy a more diverse range of habitats.

“We see this phenomenon in kefir, and then we see it’s not limited to kefir,” said Patil. “If you look at the whole world of microbiomes, cooperation is also key to their structure and function.”

References
Patil, K.R. ‘Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community.’ Nature Microbiology, Jan 2021. DOI: 10.1038/s41564-020-00816-5.

Patil, K.R. ‘Polarisation of microbial communities between competitive and cooperative metabolism.’ Nature Ecology & Evolution, Jan 2021. DOI: 10.1038/s41559-020-01353-4.

Adapted from a press release by EMBL.

New research from the ̽��ֱ�� of Cambridge and European Molecular Biology Laboratory (EMBL) shows how cooperation among bacterial species allows them to thrive as a community.

If you look at the whole world of microbiomes, cooperation is key to their structure and function.

Kiran Patil

Svorad on Wikimedia Commons

Milk kefir grains with jar of kefir in background

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. Images, including our videos, are Copyright © ̽��ֱ�� of Cambridge and licensors/contributors as identified. All rights reserved. We make our image and video content available in a number of ways – as here, on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

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Embryo development: Some cells are more equal than others even at four-cell stage

cjb250 — Thu, 24 Mar 2016 16:00:00 +0000

Once an egg has been fertilised by a sperm, it divides several times, becoming a large free-floating ball of stem cells. At first, these stem cells are ‘totipotent’, the state at which a stem cell can divide and grow and produce everything — every single cell of the whole body and the placenta, to attach the embryo to the mother’s womb. ̽��ֱ��stem cells then change to a ‘pluripotent’ state, in which their development is restricted to generating the cells of the whole body, but not the placenta. However, the point during development at which cells begin to show a preference for becoming a specific cell type is unclear.

In studies going back over ten years, Professor Magdalena Zernicka-Goetz and colleagues described how, despite the fact that cells of the four-cell stage embryo retain flexibility, each cell shows a bias in its developmental potential and fate. For example, one of the cells shows a distinct tendency to adopt the pluripotent state while another would eventually give rise to placenta. When this work was originally published, the finding proved controversial in the field as many researchers maintained that even at the four-cell embryo stage, the cells were still identical.

Now, in a study published in the journal Cell, scientists at the ̽��ֱ�� of Cambridge and the European Bioinformatics Institute (EMBL-EBI) suggests that as early as the four-cell embryo stage, the cells are indeed different.

̽��ֱ��researchers used the latest sequencing technologies to model embryo development in mice, looking at the activity of individual genes at a single cell level. They showed that some genes in each of the four cells behaved differently. ̽��ֱ��activity of one gene in particular, Sox21, differed the most between cells; this gene forms part of the ‘pluripotency network’. ̽��ֱ��team found when this gene’s activity was reduced, the activity of a master regulator that directs cells to develop into the placenta increased.

“We know that life starts when a sperm fertilises an egg, but we’re interested in when the important decisions that determine our future development occur,” says Professor Magdalena Zernicka-Goetz from the Department of Physiology, Development and Neuroscience at the ̽��ֱ�� of Cambridge. “We now know that even as early as the four-stage embryo – just two days after fertilisation – the embryo is being guided in a particular direction and its cells are no longer identical.”

Dr John Marioni of EMBL-EBI, the Wellcome Trust Sanger Institute and the Cancer Research UK Cambridge Institute, adds: “We can make use of powerful sequencing tools to deepen our understanding of the molecular mechanisms that drive development in individual cells. Because of these high-resolution techniques, we are now able to see the genetic and epigenetic signatures that indicate the direction in which early embryonic cells will tend to travel.”

̽��ֱ��research was funded by the Wellcome Trust, the European Molecular Biology Laboratory and Cancer Research UK.

Reference
Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in Four-Cell Mouse Embryos. Cell; 24 March 2016. DOI: 10.1016/j.cell.2016.01.047

Genetic ‘signatures’ of early-stage embryos confirm that our development begins to take shape as early as the second day after conception, when we are a mere four cells in size, according to new research led by the ̽��ֱ�� of Cambridge and EMBL-EBI. Although they seem to be identical, the cells of the two day-old embryo are already beginning to display subtle differences.

We now know that even as early as the four-stage embryo – just two days after fertilisation – the embryo is being guided in a particular direction and its cells are no longer identical

Magdalena Zernicka-Goetz

Zernick-Goetz lab, ̽��ֱ�� of Cambridge

4-cell stage embryo

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Cooperation is key to success in microbial communities

Embryo development: Some cells are more equal than others even at four-cell stage