Monday, May 05, 2025

 

AI plays detective to help scientists find hidden microbes



New machine learning tool redefines microbial rare biosphere



University of Ottawa

AI plays detective to help scientists find hidden microbes 

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“With ulrb, we’ve created a method that is precise, adaptable, and capable of improving biodiversity assessments”

Paula Branco

— Associate Professor, School of Electrical Engineering and Computer Science

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Credit: University of Ottawa




A team of researchers has created a novel machine learning tool that's cracking open one of biology's trickiest puzzles: finding the rarest microbes on Earth. Think of it like finding a needle in a haystack, except the needle is microscopic and might hold the key to how our ecosystems work.

The tool, called ulrb, uses AI to spot these elusive microorganisms that, despite their tiny numbers, pack a serious punch in keeping our planet's ecosystems healthy. It's like having a super-smart detective that can pick out the rare gems from billions of other microbes.

This pioneering open-source software, developed through collaboration between the University of OttawaDalhousie universityInterdisciplinary Center for Marine and Environmental Research (CIIMAR), Institute for Bioengineering and Biosciences of Instituto Superior Técnico, and the University of Porto,  addresses long-standing challenges in microbial ecology and opens new doors for ecological research.

“This tool solves a major issue in microbial ecology: how do we define rare microorganisms?” says co-author Paula Branco, Associate Professor at the University of Ottawa’s School of Electrical Engineering and Computer Science. “With ulrb, we’ve created a method that is precise, adaptable, and capable of improving biodiversity assessments. Before, we were basically guessing at what counted as 'rare' in the microbial world. Now we have a precise way to figure it out.”

“Our findings show that ulrb not only identifies rare microorganisms but also works with non-microbial data, such as tree census datasets,” explains Francisco Pascoal, PhD Candidate at CIIMAR (Interdisciplinary Center for Marine and Environmental Research), who led the development of the ulrb R package as part of his doctoral research. “This versatility makes it a powerful tool for ecological applications.”

Conducted entirely computationally, the study tested ulrb against various microbiome datasets. The software demonstrated statistical robustness and practical applications, such as characterizing coral microbiomes.

Available as open-source software on CRAN and GitHubulrb includes tutorials to assist users worldwide. Its impact extends beyond academia by enhancing biodiversity assessments and aiding evaluations of climate change effects on microbial communities.

The project, initiated in 2022, has recently been published in Communications Biology under the title Definition of the microbial rare biosphere through unsupervised machine learning. marking a new chapter in how we study the hidden world of microorganisms.

 

Adolescents with mental health conditions use social media differently than their peers, study suggests




University of Cambridge





Young people with a diagnosable mental health condition report differences in their experiences of social media compared to those without a condition, including greater dissatisfaction with online friend counts and more time spent on social media sites.

This is according to a new study led by the University of Cambridge, which suggests that adolescents with “internalising” conditions such as anxiety and depression report feeling particularly affected by social media.

Young people with these conditions are more likely to report comparing themselves to others on social media, feeling a lack of self-control over time spent on the platforms, as well as changes in mood due to the likes and comments received.

Researchers found that adolescents with any mental health condition report spending more time on social media than those without a mental health condition, amounting to an average of roughly 50 minutes extra on a typical day.*

The study, led by Cambridge’s Medical Research Council Cognition and Brain Sciences Unit (MRC CBU), analysed data from a survey of 3,340 adolescents in the UK aged between 11 and 19 years old, conducted by NHS Digital in 2017.**

It is one of the first studies on social media use among adolescents to utilise multi-informant clinical assessments of mental health. These were produced by professional clinical raters interviewing young people, along with their parents and teachers in some cases.***  

“The link between social media use and youth mental health is hotly debated, but hardly any studies look at young people already struggling with clinical-level mental health symptoms,” said Luisa Fassi, a researcher at Cambridge’s MRC CBU and lead author of the study, published in the journal Nature Human Behaviour.

“Our study doesn’t establish a causal link, but it does show that young people with mental health conditions use social media differently than young people without a condition.

“This could be because mental health conditions shape the way adolescents interact with online platforms, or perhaps social media use contributes to their symptoms. At this stage, we can’t say which comes first – only that these differences exist,” Fassi said.

The researchers developed high benchmarks for the study based on existing research into sleep, physical activity and mental health. Only findings with comparable levels of association to how sleep and exercise differ between people with and without mental health conditions were deemed significant.

While mental health was measured with clinical-level assessments, social media use came from questionnaires completed by study participants, who were not asked about specific platforms.****

As well as time spent on social media, all mental health conditions were linked to greater dissatisfaction with the number of online friends. “Friendships are crucial during adolescence as they shape identity development,” said Fassi.

“Social media platforms assign a concrete number to friendships, making social comparisons more conspicuous. For young people struggling with mental health conditions, this may increase existing feelings of rejection or inadequacy.”

Researchers looked at differences in social media use between young people with internalising conditions, such as anxiety, depression and PTSD, and externalising conditions, such as ADHD or conduct disorders.

The majority of differences in social media use were reported by young people with internalising conditions. For example, “social comparison” – comparing themselves to others online – was twice as high in adolescents with internalising conditions (48%, around one in two) than for those without a mental health condition (24%, around one in four).

Adolescents with internalising conditions were also more likely to report mood changes in response to social media feedback (28%, around 1 in 4) compared to those without a mental health condition (13%, around 1 in 8). They also reported lower levels of self-control over time spent on social media and a reduced willingness to be honest about their emotional state when online.*****

“Some of the differences in how young people with anxiety and depression use social media reflect what we already know about their offline experiences. Social comparison is a well-documented part of everyday life for these young people, and our study shows that this pattern extends to their online world as well,” Fassi said.

By contrast, other than time spent on social media, researchers found few differences between young people with externalising conditions and those without a condition.

“Our findings provide important insights for clinical practice, and could help to inform future guidelines for early intervention,” said Cambridge’s Dr Amy Orben, senior author of the study.

“However, this study has only scratched the surface of the complex interplay between social media use and mental health. The fact that this is one of the first large-scale and high-quality studies of its kind shows the lack of systemic investment in this space.”

Added Fassi: “So many factors can be behind why someone develops a mental health condition, and it's very hard to get at whether social media use is one of them.”

“A huge question like this needs lots of research that combines experimental designs with objective social media data on what young people are actually seeing and doing online.”

“We need to understand how different types of social media content and activities affect young people with a range of mental health conditions such as those living with eating disorders, ADHD, or depression. Without including these understudied groups, we risk missing the full picture.”

-ENDS-

Notes:

*Study participants were asked to rate their social media use on a typical school day and a typical weekend or holiday day. This was given as a nine-point scale, ranging from less than 30 minutes to over seven hours. Responses from adolescents with any mental health condition approached on average "three to four hours," compared to adolescents without a condition, who averaged between "one to two hours" and "two to three hours."

The category of all mental health conditions in the study includes several conditions that are classed as neither internalising or externalising, such as sleep disorders and psychosis. However, the numbers of adolescents suffering from these are comparatively small.

**The survey was conducted as part of NHS Digital’s Mental Health of Children and Young People Survey (MHCYP) and is nationally representative of this age group in the UK. The researchers only used data from those who provided answers on social media use (50% male, 50% female).

*** Previous studies have mainly used self-reported questionnaires (e.g. a depression severity questionnaire) to capture mental health symptoms and conditions in participants.

**** The researchers point out that, as responses on social media use were self-reported, those with mental health conditions may be perceiving they spend more time on social media rather than actually doing so. They say that further research with objective data is required to provide definitive answers.

***** For data on social media use, study participants were asked to rate the extent to which they agree with a series of statements on a five-point Likert scale. The statements ranged from “I compare myself to others on social media” to “I am happy with the number of friends I have on social media”.

Researchers divided responses into 'disagree' (responses 1 to 3) and 'agree' (responses 4 and 5) and then calculated the proportion of adolescents agreeing separately for each diagnostic group to aid with public communication of the findings.

Once the embargo lifts, the paper will be available at the following URL: https://doi.org/10.1038/s41562-025-02134-4

 

Depressive symptoms among U.S. adults



JAMA Internal Medicine





About The Study: In this study, the prevalence of depressive symptoms increased substantially among U.S. adults during the COVID-19 pandemic. Worsening mental health trends were concentrated among younger adults. 



Corresponding Author: To contact the corresponding author, Rishi K. Wadhera, MD, MPP, MPhil, email rwadhera@bidmc.harvard.edu.

To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/

(doi:10.1001/jamainternmed.2025.0993)

Editor’s Note: Please see the article for additional information, including other authors, author contributions and affiliations, conflict of interest and financial disclosures, and funding and support.

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https://jamanetwork.com/journals/jamainternalmedicine/fullarticle/10.1001/jamainternmed.2025.0993?guestAccessKey=9afe4d29-95ee-4fdc-8397-acbea9b85193&utm_source=for_the_media&utm_medium=referral&utm_campaign=ftm_links&utm_content=tfl&utm_term=050525

 

Beef production emits more than twice the greenhouse gas targets



In an article published in Environmental Science and Pollution Research, researchers from the Federal University of São Paulo discuss the need for the production chain to adopt emission reduction practices




Fundação de Amparo à Pesquisa do Estado de São Paulo





One of the pillars of the Brazilian economy and one of the sectors responsible for the highest greenhouse gas emissions, beef production in Brazil, as it is currently practiced, emits more than twice the limit needed to meet international environmental targets. This is one of the conclusions of a study published in the journal Environmental Science and Pollution Research.

The work includes an evaluation of projected emissions scenarios, along with an economic assessment. The researchers calculated that the sector’s emissions could range from 0.42 to 0.63 gigatons of CO2 equivalent (GtCO2e) by 2030, while the limit for meeting the Nationally Determined Contribution (NDC) target would be 0.26 GtCO2e. On the other hand, mitigation strategies along the production chain could prevent losses of up to USD 42.6 billion and ensure greater competitiveness.

The NDCs are the commitment that countries made in the Paris Agreement, signed in 2015, and which will be reviewed this year leading up to COP30 (United Nations Climate Change Conference) in Belém, in the Brazilian Amazon.

The commitment includes emission reduction targets for countries, with guidelines for transforming the development model, covering all sectors of the economy. The global objective is to limit the increase in the planet’s average temperature to 1.5 °C compared to the pre-industrial period (between 1850 and 1900). This limit, however, is being put at risk – 2024 was the hottest year in history, with an average global temperature increase of 1.55 °C, according to the World Meteorological Organization (WMO).

The study was based on the NDC in force until 2024 – a 43% reduction in emissions by 2030 compared to 2005 levels. In November, Brazil submitted its new contribution to the United Nations Framework Convention on Climate Change (UNFCCC), committing to reduce net greenhouse gas emissions by between 850 million and 1.05 billion tons of CO2 equivalent by 2035 – a 59% to 67% reduction from 2005 levels.

“We know how important the beef sector is not only for the economy but also for the Brazilian menu. Our goal is not to say: produce or eat less meat, but to start a discussion about the current form of production, which is linked to deforestation, high emissions and without adopting sustainable techniques. That’s not the way to achieve our climate targets. Our findings show that it’s necessary to adopt practices in the production chain that reduce emissions. This also contributes to reducing the costs associated with climate change,” says the article’s first author, biologist Mariana Vieira da Costa, from the Laboratory of Economics, Health and Environmental Pollution (LESPA) at the Federal University of São Paulo (UNIFESP) in Brazil.

In their work, the authors used the so-called social cost of carbon (SCC), a way of quantifying the financial impact of emissions on society and a reference for climate policy and decision-making.

The SCC represents the economic cost of emitting one ton of CO2, including non-commercial impacts on the environment and human health, and incorporating consequences such as agricultural losses and damage from extreme weather events. These costs can be reduced or redirected to investments in more sustainable livestock production practices through public policies and accessible credit lines.

According to the study, the potential cost savings range from USD 18.8 billion to USD 42.6 billion by 2030, depending on whether the targets are met.

In 2023, Brazil set a record for beef exports, selling 2.29 million tons to 157 countries and generating USD 10.55 billion in sales. The scientists considered the importance of beef exports to Brazil by calculating how much would be available for domestic consumption in 2030 if production were reduced to stay within the 0.26 GtCO2e emission limit needed to meet the NDC. The result was between 2 and 10 kg of beef per capita (per year).

“I’ve always wanted to study the relationship between cattle farming and climate change. At first, we had trouble finding more refined data. That’s why we created our indicator,” adds Costa, who was supervised by Professor Simone Miraglia, head of LESPA-UNIFESP and co-author of the article with biologist Daniela Debone.

For Miraglia, the results are important because, without significant reductions in greenhouse gas emissions, the increase in the global average temperature will lead to additional economic impacts, such as a reduction in agricultural production, an increase in forest fires and an increase in health impacts, including mortality.

Scenario

In a period of almost four decades (1985 to 2022), the agricultural area in Brazil has grown by 50% to 282.5 million hectares – a third of the national territory. Of this total, 58% is pasture (currently at 164.3 million hectares), according to a study by MapBiomas, a collaborative network made up of NGOs, universities and technology startups that maps land cover and land use in Brazil.

About 64% of the expansion of agriculture was due to deforestation for pasture (64.5 million hectares). This growth occurred mainly in the Amazon, causing the biome to overtake the Cerrado (Brazil’s savannah-like biome) in terms of pasture area.

The scientists point to the need for synergy between research and rural producers to promote more efficient, low-emission production practices and to seek environmentally sustainable techniques and technologies. They also highlight the role that the federal government can play in brokering and integrating research and technology adoption by producers.

They point out that although the ABC+ Plan currently facilitates investments in intensive practices by livestock farmers, their adoption is still low. The Plan for Adaptation and Low Carbon Emissions in Agriculture (ABC+) is an agenda of the Brazilian government to be implemented between 2020 and 2030, which provides continuity to the sectoral policy to combat climate change in the agricultural sector. In addition to creating and strengthening mechanisms for the adoption of sustainable production systems and practices, it seeks to diversify financial and fiscal sources and instruments.

Costa points out that the diversification of incentives, such as tax exemptions and the introduction of carbon credits, is essential to stimulate and promote significant changes on a large scale in the sector.

The work was supported by FAPESP through a scholarship for Costa and another project with an approach to analyzing greenhouse gas emissions, climate change and health indicators.

About FAPESP

The São Paulo Research Foundation (FAPESP) is a public institution with the mission of supporting scientific research in all fields of knowledge by awarding scholarships, fellowships and grants to investigators linked with higher education and research institutions in the state of São Paulo, Brazil. FAPESP is aware that the very best research can only be done by working with the best researchers internationally. Therefore, it has established partnerships with funding agencies, higher education, private companies, and research organizations in other countries known for the quality of their research and has been encouraging scientists funded by its grants to further develop their international collaboration.