New tool closes gap on untapped potential of phages

University of Otago

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A new tool to mutate bacteriophages – viruses that infect bacteria – provides a “big leap” forward in both our understanding of how they function, and our ability to harness their full potential.

Developed by researchers in the University of Otago – Ōtākou Whakaihu Waka, New Zealand, Department of Microbiology and Immunology, the method features on the latest cover of prestigious international journal Nature Microbiology.

Senior author Professor Peter Fineran says bacteriophages, or simply phages, have “huge potential” to combat the antimicrobial resistance crisis, and for increasing sustainable agriculture as an alternative to agrochemicals, because they can destroy bacteria.  

“But our knowledge of phages is probably like the understanding of antibiotics back in the 1950s. Many phage genes are currently in the area of microbial dark matter – encoding functions we just don’t understand – which is limiting our ability to use phages in healthcare and biotechnology.

“This new development is a big leap in how we can rapidly understand phage biology and then use that knowledge to make phages work better to help achieve our goals.” 

Co-lead author Dr Manuela Fuchs says the new method allows for genome-wide mutagenesis of bacteriophages using CRISPR-Cas technology.

The researchers utilised transposon insertion sequencing – using a mobile piece of DNA which can jump in and disrupt a gene – combined with CRISPR-anti-CRISPR-based selection, to select phages that have been mutated. This allows them to identify genes that are essential and genes that are non-essential for phage survival.

“Once we had that established, we thought we could expand the technique and also use it to add genes directly into the phage genomes. We essentially found it is possible to load additional genes on that transposon, not just our anti-CRISPR protein. While we added a fluorescent marker, it could be used to, for example, add additional anti-defence genes to phages, to improve their therapeutic potential,” Dr Fuchs says.

Senior author Dr Leah Smith says the method enables genes to be automatically inserted somewhere while maintaining phage function.

“This is a systematic, broadly applicable, and cost-effective way to not only investigate gene function, but also rapidly engineer phage genomes.

“This opens up new opportunities for both fundamental research and future therapeutic development.”

One particular example of this would be biofilms, which can cause hard-to-treat infections on prosthesis implants and medical devices.

“With this new technique, we could quickly load phages to have more things that stop some bacterial defences so that they can be harnessed to kill pathogens more easily,” Dr Smith says.

Funding: 

This research was supported by Professor Fineran’s Royal Society of New Zealand – Te Apārangi James Cook Research Fellowship, Dr Smith’s Royal Society Marsden Fund grant and L’Oréal-UNESCO For Women in Science Fellowship, Dr Fuchs’ Feodor Lynen Research Fellowship from the Alexander von Humboldt Stiftung, and Natalie Kyte’s University of Otago Doctoral Scholarship.
 

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Journal

Nature Microbiology

DOI

10.1038/s41564-026-02486-1

Article Title

Defining the essential genome of diverse phages with phage Tn-seq

Article Publication Date

25-Sep-2026

 

Beyond “normal” and “abnormal”: Health checkup values show nonlinear links to future healthcare costs

Kanazawa University

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Figure1. Study overview: Visualizing associations between health checkup data and healthcare costs 3–4 years later

Specific Health Checkup data were linked with National Health Insurance Database (KDB) claims data. Using generalized additive models, the study visualized nonlinear and sex-specific associations between routine health checkup measures and healthcare costs 3–4 years later. HbA1c showed a stronger association with future healthcare costs above approximately 6.0%.

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Credit: Kanazawa University (2026)

As populations age and healthcare expenditures continue to rise worldwide, there is growing interest in understanding how routinely collected health data may help characterized future healthcaaare needs and costs. 

A multidisciplinary research team led by Kanazawa University investigated how routinely collected health checkup measurements are associated with healthcare costs several years later. The researchers linked Specific Health Checkup data with claims data from Japan’s National Health Insurance Database (KDB) and analyzed 6,757 adults aged 60–74 years, corresponding to 11,148 person-years of observation.

Using generalized additive models (GAMs), which can capture curved rather than strictly linear relationships, the team examined associations between health indicators measured at checkups and outpatient, inpatient, and prescription-drug costs incurred 3–4 years later.

Age and glycated hemoglobin (HbA1c) showed consistent associations with future healthcare costs in both men and women. In particular, HbA1c showed a J-shaped pattern, with the association becoming stronger above approximately 6.0%. Body mass index (BMI), waist circumference, and fatty liver index (FLI) were also associated with future healthcare costs, but the patterns differed by sex.

In men, waist circumference and FLI showed relatively prominent associations with future healthcare costs. In women, stronger associations were observed at higher levels of BMI and waist circumference. These findings indicate that the relationship between health checkup values and later healthcare expenditure cannot always be adequately described by a simple straight line.

A key feature of the study is that it visualizes the ranges of health checkup values in which associations with future healthcare costs become stronger, rather than interpreting each measurement only as “normal” or “abnormal.” These findings characterize population-level associations between health checkup values and future healthcare costs, rather than providing precise predictions of individual healthcare costs.

The researchers plan to integrate additional information, including disease history, prescribed medications, healthcare utilization, and lifestyle factors, to develop more comprehensive approaches to health-risk assessment and preventive planning.

Researcher Quote

“Many health checkup results are just numbers, and this can make it difficult for people to connect them with their own health, especially for lifestyle-related diseases that may progress without noticeable symptoms. Healthcare costs offer a different perspective by expressing future health burden in an economic dimension. By showing how checkup values are associated with later medical spending, we hope to provide another way for people to reflect on their health. Although this study did not directly examine behavior change, such information may eventually help support preventive action and the design of community health programs,” said Shigehiro Karashima, the corresponding author.

Funding

This study was partially supported by collaborative research funding from System Support Co., Ltd. (Kanazawa, Japan). The funder had no role in the study design, data collection, analysis, interpretation, or writing of the manuscript.

 

 

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Journal

Health Economics Review

DOI

10.1186/s13561-026-00818-9

Article Title

Nonlinear modeling of health checkup factors and future claims-based healthcare costs in Japan: a retrospective cohort study

 

New tools pinpoint where urban trees could provide the most relief from heat

By combining high-resolution satellite heat mapping with shade and equity modelling, UBC researchers are helping city planners target trees where they can have the greatest impact

University of British Columbia

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Todd Cashin and Jennifer Miles of the City of Kelowna and UBC's Dr. Melissa McHale lead a walking tour of Rutland with researchers and city staff, assessing tree-planting challenges in the neighbourhood.

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Credit: Photo credit: Melissa McHale

Cities trying to cool sweltering streets often set broad tree canopy targets. But those targets can overlook the reality that not all shade is equally useful, and not every neighbourhood has room for more trees. 

Now, two new studies from University of British Columbia researchers offer a more targeted approach. Tested in Kelowna, B.C., the complementary tools can identify urban hot spots down to individual blocks and determine where new trees could deliver the greatest benefits. 

“Cities often know they need more tree canopy, but they still have to decide exactly where planting is possible and where shade will make the greatest difference,” said Dr. Melissa McHale, a professor in UBC’s Faculty of Forestry and Environmental Stewardship and senior author on both studies. “Together, these approaches move us from broad citywide targets toward decisions at the scale of the streets and neighbourhoods where people actually experience heat.” 

Unmasking ‘hidden’ heat 

Satellite thermal maps give cities a bird’s-eye view of surface temperatures, but often lack the detail needed for block-by-block planning. Standard 30-metre pixels can blend the temperatures of rooftops, asphalt, lawns and tree canopy into a single average. 

In the first study, published in Remote Sensing, UBC researchers tested an open-source machine-learning technique that sharpens imagery from Landsat and Sentinel-2 satellites to 10-metre resolution. 

The higher-resolution maps revealed nearly five times as much temperature variation across Kelowna. With conventional 30-metre imagery, hot spots appeared in broad areas averaging 18,000 square metres, roughly two and a half Canadian football fields. The 10-metre approach detected much smaller hot spots as small as 700 square metres, about the footprint of a large residential lot. 

Features of the landscape like tree canopy and paved surfaces explained more than 65 per cent of the additional temperature detail, indicating the method was detecting real landscape differences rather than digital noise. While surface temperature is not the same as air temperature, the freely available approach could help cities identify small hot spots that conventional mapping misses. 

Putting shade where it counts — and fits 

Finding heat is only part of the challenge; cities also need to know where trees can realistically be planted and provide useful shade. 

In the second study, published in Urban Forestry & Urban Greening, the team used CanopyFit, a modelling approach conceived and spearheaded by Dr. McHale and developed collaboratively with the Urban Ecology and Sustainability Lab and her municipal partners, to map practical planting potential. It excludes areas unsuitable for planting, such as buildings, sports fields, underground utilities, wildfire buffer zones and environmentally sensitive ecosystems, then assesses shade potential alongside heat exposure and social and economic need. 

Across Kelowna, the model identified space for 248 hectares of potential new mature canopy, but that opportunity was highly uneven. Just 20 per cent of the analyzed area accounted for more than half (50.8 per cent) of all potential shade gains. 

The analysis also points to different solutions for different neighbourhoods. Some are “win-win” areas, where high heat and equity needs coincide with ample planting space, identifying areas where additional tree planting could deliver particularly large benefits.” Others face high heat and greater need but have little room for new trees, suggesting alternatives such as removing asphalt, changing development rules or installing engineered shade. 

Because both approaches use adaptable frameworks and widely available data, municipalities elsewhere can combine them with local information to develop strategies for reducing heat. 

“Cities have limited space and resources for planting, so we need to be strategic,” said Dr. McHale. “The goal is to establish and sustain large, healthy trees where their cooling and other benefits are needed most. Where the built environment leaves little room for trees, the findings can help cities identify barriers to planting and assess other approaches to providing shade.” 

 

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Journal

Urban Forestry & Urban Greening

Method of Research

Imaging analysis

Subject of Research

Not applicable

Article Title

Putting shade where it counts: A classification approach for prioritizing tree planting locations using heat equity and shade modelling

Article Publication Date

1-Nov-2026

“Public reputation” or “Personal experience”?

How people evaluate others when reputation and personal experience conflict

Rissho University

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This image was created using generative AI.

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Credit: Credit: Hitoshi Yamamoto at Rissho university

A research team led by Professor Hitoshi Yamamoto of Rissho University experimentally examined how people evaluate others when the public reputation of the person involved in an interaction conflicts with their own personal experience with that person. The study was published in the international journal Evolution and Human Behavior on September 14, 2026.

In human societies, people often rely on reputation when deciding whom to help or cooperate with. This reputation-based mechanism for supporting cooperation is known as indirect reciprocity. The present study examined how people’s judgments change when reputational information is combined with their own direct experience.

The researchers conducted two scenario-based experiments with participants in Japan, using situations involving coworkers at a restaurant and neighbors in a community. Participants were shown a situation in which one person either cooperated with or refused a request from another person. The researchers varied both the reputation of the person making the request and whether that person had previously cooperated with or refused to cooperate with the participant, and then examined how participants evaluated the person who responded to the request.

The results showed that when someone refused to cooperate with another person, evaluations of that refusal varied depending on the participant’s prior experience with the person who refused. For example, even when that person had a bad public reputation, refusal was evaluated more negatively if the person had previously helped the participant. Conversely, even when the person had a good reputation, refusal was evaluated more positively if that person had previously refused to help the participant. In other words, when reputation and personal experience conflicted, personal experience was strongly reflected in evaluations of non-cooperation.

By contrast, cooperative behavior was generally evaluated positively regardless of the other person’s reputation or the participant’s own experience with them. This suggests that people do not evaluate cooperation and non-cooperation in the same way: when judging non-cooperation in particular, they place greater weight on how the person on the receiving end had previously treated them.

The study also found that even when the person being refused had a bad reputation and had previously refused to cooperate with the participant—a situation in which there appeared to be good reason not to cooperate—the refusal itself was evaluated neutrally rather than positively. This suggests that even when there is a reason to refuse cooperation, people do not necessarily regard such behavior as positively “good.”

Previous research on indirect reciprocity, in which people use reputation to decide whom to cooperate with, has focused mainly on socially shared reputational information. In everyday relationships, however, public reputation and personal experience do not always match: someone may be well regarded by others but have treated us poorly, or may have a bad reputation despite having helped us personally. This study shows how people combine these two sources of information when evaluating others.

 

Professor Yamamoto commented:

“In everyday life, we judge others by combining many different kinds of information, including what we hear about them from others and what we have experienced ourselves. Our study provides one clue to understanding how people make judgments when these sources of information do not agree. In future research, we would like to examine how people use reputational information in environments where direct personal experience is limited, such as online rating systems and AI-mediated judgments.”

Read more:https://doi.org/10.1016/j.evolhumbehav.2026.106980
Yamamoto, H., Suzuki, T., & Okada, I. (2026). Direct experience overrides reputation in evaluations of defection in indirect reciprocity. Evolution and Human Behavior, 47(6), 106980.

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Journal

Evolution and Human Behavior

DOI

10.1016/j.evolhumbehav.2026.106980

Article Title

Direct experience overrides reputation in evaluations of defection in indirect reciprocity

Article Publication Date

24-Sep-2026

 

High-tech canopy maps reveal how tropical birds use Amazon forests

New method helps land managers anticipate ecological change and prioritize conservation work

Arizona State University

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Researchers mapped chemical and structural differences in forest canopies across Peru using the ASU Global Airborne Observatory.

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Credit: Greg Asner/Arizona State University

Tropical forests may look like a uniform sea of green from above, but new research shows that carefully measured differences in forest structure and function can help explain how birds use existing habitats, how they respond to threats, and which communities may be most at risk as forests change.

Using aircraft-mounted sensors, researchers mapped chemical and structural differences in forest canopies across Peru. They then compared those forest types with the ranges and traits of more than 1,300 forest-dependent bird species.

“By combining advanced airborne imaging spectroscopy with ecological data, we aren’t just mapping where the trees are; we are mapping the diversity and composition of the canopy itself and how the ecosystem functions,” said senior author Greg Asner, director of the ASU Center for Global Discovery and Conservation in the Julie Ann Wrigley Global Futures Laboratory.

“This approach provides a scalable way to identify distinct conservation risk areas across previously undocumented forest types, providing explanatory power far beyond traditional forest cover maps,” Asner said. He and co-authors at The Australian National University published the findings in Nature Communications.

As deforestation, climate change and land-use pressures continue to reshape tropical forests, the researchers said the method could help land managers anticipate ecological change and prioritize strategies that protect both species diversity and ecosystem function.

“By linking newer high-tech maps of the chemical and functional traits of the forest canopy to avian ecology, we demonstrated that the composition of the trees exerts a big influence on the life-history strategies and vulnerabilities of the bird communities living there,” said first author George Olah, a DECRA fellow at the Fenner School of Environment and Society at The Australian National University.

The research builds on a pioneering effort by Asner and colleagues to map forests from the air by measuring chemical signatures of the tree canopy. Their aircraft-mounted spectrometer measured the wavelengths of light reflected by foliage. This allowed the researchers to measure seven features of forest canopies, including leaf nutrients, water content and plant compounds. The researchers used those measurements to sort Peru’s forests into six broad forest types.

For the new study, the team looked at where 1,331 forest-dependent bird species live and measured how much of each species’ range fell within those six forest types. They then compared those patterns with information about each bird, including body size, clutch size, where it feeds in the forest, conservation status and population trend.

The goal was to see whether differences in the forest canopy could help explain differences in the birds that live there, including which species may be more vulnerable as forests are cleared or changed.

Peru is home to about 18% of the world’s bird species, many of them dependent on forest habitats that cover more than 60% of the country.

The researchers found that birds in northern Amazonian swamp forests tended to be larger-bodied and longer-lived, traits associated with slower reproductive strategies and potentially lower ecological resilience. Montane Andean forests were more often home to understory specialists, which can be more sensitive to habitat fragmentation and changes in temperature and humidity. Birds in lower Andean forests showed stronger links to cumulative human threats, while floodplain forest birds showed traits associated with greater tolerance of urbanization.

These findings can help focus conservation efforts to where they are most needed. If conservation networks prioritize areas based solely on total species richness or generic tree cover, they might over emphasize protections for resilient floodplain forests while leaving large-bodied birds of the swamp forests relatively unprotected.

Remotely sensed canopy traits can help scientists move beyond counting species to better understand the functional integrity and resilience of ecosystems. The approach could support expanded biodiversity monitoring across the Amazon Basin, especially as satellite-based imaging spectroscopy becomes more widely available.

“By integrating habitat functionality with species traits, we can revolutionize conservation planning at the landscape scale,” Olah said.

“Mapping the biological and functional diversity of the Amazon canopy is essential to safeguard the full spectrum of avian ecological roles, preventing the silent loss of animals as the forest is either protected or deforested,” Asner said.

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Journal

Nature Communications

DOI

10.1038/s41467-026-77135-6

Method of Research

Data/statistical analysis

Subject of Research

Not applicable

Article Title

Canopy functional composition shapes bird traits and vulnerability in tropical Peruvian forests

Article Publication Date

25-Sep-2026