Microbes in breast milk help populate infant gut microbiomes

University of Chicago Medical Center

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Illustration by Pamela Ferretti

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Credit: Illustration by Pamela Ferretti

Most conversations about breast milk tend to focus on topics like nutrients, antibodies and bonding time rather than bacteria. But it turns out that human milk carries its own tiny community of microbes, and those passengers may help shape a baby’s developing gut microbiome — which in turn can impact nutrient absorption, metabolic regulation, immune system development, and more.

A new study published in Nature Communications provides one of the most detailed portraits yet of how different combinations of bacteria in human milk contribute to the assembly of infants’ gut microbiomes.

Mapping the milk microbiome

The breast milk microbiome is notoriously difficult to analyze because the milk’s high fat content and relatively low bacterial load complicate the process of extracting genomic material.

“Breast milk is the recommended sole source of nutrition for an infant’s first months of life, but important questions about the milk microbiome remained unanswered because the analytical challenges are intimidating,” said first author Pamela Ferretti, PhD, a postdoctoral researcher in the Blekhman Lab at the University of Chicago. “We decided to tackle this endeavor because our collaboration presented a unique opportunity to combine key resources.”

Those resources included hundreds of milk samples collected as part of the Mothers and Infants LinKed for Healthy Growth (MILk) study, led by Ellen Demerath, PhD, at the University of Minnesota and by David Fields, PhD, at the Oklahoma University Health Sciences Center. On the UChicago side, Ferretti and her colleagues had access to metagenomic tools and deep experience with microbiome data, including Ferretti’s highly specific expertise in infant microbiomes and transmission analysis. In her previous research, she studied how different maternal body sites — such as mouth, skin, and vaginal cavity — contributed to infant microbiomes.

Analyzing 507 breast milk and infant stool samples from 195 mother–infant pairs, the team found that breast milk contained a distinct mix of bacterial species dominated by the genus bifidobacteria, including Bifidobacterium longum, B. breve, and B. bifidum. More than half of the milk samples carried B. longum, a species abundant in over 98% of the infants’ gut microbiomes.

“Even though B. longum is well-documented as being highly prevalent in the infant gut, it was surprising to find such a strong signature of that species in the breast milk samples because previous milk studies mostly reported other bacterial taxa like Staphylococcus and Streptococcus,” Ferretti said. “We think these results will prompt some reevaluation in the field.”

Tracing microbes from milk to the infant gut

Most prior studies analyzing bacterial DNA in breast milk used a relatively inexpensive, fast technique called amplicon sequencing, which targets a limited number of predetermined genomic regions for each experiment. This method is good for efficiently identifying species within a mixed sample, but it leaves most of the bacterial genome unexamined.

“Metagenomic analysis is trickier and more complicated, but it really paid off because it allowed us to obtain information at the level of different bacterial strains — which is key, because that’s the only level where we could actually claim to know about transmission,” Ferretti said.

The paper reported 12 instances in which the same exact strain was found in a mother’s breast milk and in the gut of her infant, which is a very strong indication that the transmission happens vertically via breastfeeding.

Some of these shared strains were beneficial commensal species such as B. longum and B. bifidum, which help digest human milk sugars and support healthy gut development. Others, however, were pathobionts — microbes like E. coli and Klebsiella pneumoniae that can live harmlessly in healthy individuals but have the potential to cause infection under certain conditions. The authors note that all mothers and infants in the study were healthy, indicating that these species’ presence in milk does not inherently signal disease but rather reflects the microbial diversity that can be transferred during breastfeeding.

Interestingly, the team also saw specific strains of bacteria usually associated with the mouth — such as Streptococcus salivarius and Veillonella species — in milk samples. They realized this as potential evidence of “retrograde flow” during breastfeeding: as the baby feeds, tiny amounts of oral bacteria may travel back into the nipple and ducts and become part of the milk microbiome.

Expanding human milk research

Ferretti noted that the study not only sheds light on microbial transmission but also fills a major gap in available data for scientists studying early-life health.

“This study nearly doubled the number of metagenomic breast milk samples that are publicly available, and pairs them with extensive information on mothers’ health and lifestyle,” Ferretti said. “We’re hopeful that our findings and future analyses that use this dataset will really push the field forward.”

In subsequent studies, the researchers hope to take their analysis to the next level with a multi-omic approach, including analyzing metabolites like human milk oligosaccharides (HMOs) and examining the “exposome” of environmental factors like PFAS and antimicrobial resistance that can be passed along through milk.

“Ultimately, we’re interested in looking at longer health trajectories to see if factors in breast milk and early life are predictive of health outcomes later in life,” Ferretti said.

 

“Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother’s milk” was published early access in November 2025 in Nature Communications. Co-authors include Pamela Ferretti, Mattea Allert, Kelsey E. Johnson, Marco Rossi, Timothy Heisel, Sara Gonia, Dan Knights, David A. Fields, Frank W. Albert, Ellen W. Demerath, Cheryl A. Gale and Ran Blekhman.

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Journal

Nature Communications

DOI

10.1038/s41467-025-66497-y 

Method of Research

Observational study

Subject of Research

Human tissue samples

Article Title

Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother’s milk

AMERIKA (OF COURSE)

New study highlights link between eviction rates and gun violence

University of Chicago

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Violent crime has fallen to historic lows in Chicago, although gun violence continues to plague neighborhoods with concentrated poverty. A 2023 study of five major cities showed that more than 55% of shootings occurred in just 9% of total census tracts, and that small increases in things like poverty, unemployment, or limited access to health care are associated with large increases in firearm violence.

Yet not every neighborhood that struggles with these challenges also has high rates of violence. What is different about these communities? A key factor may be eviction rates. A new study from the University of Chicago looks at the link between evictions and gun violence across Chicago and found that every 1% increase in eviction rate in a census tract was associated with 2.66 more shootings.

The study also showed that evictions disrupt a neighborhood’s “collective efficacy,” or residents’ shared belief in their ability to work together for the common good. This sense of cohesion or neighborliness can protect disadvantaged neighborhoods from gun violence in spite of greater socioeconomic disadvantages.

“Evictions really break up communities, both for the people who are forced to move and for people who are losing their neighbors,” said Thomas Statchen, a medical student at the University of Chicago Pritzker School of Medicine and lead author of the study, published recently in JAMA Network Open. “Here we can see that eviction rates not only impact these social characteristics but are associated with increased gun violence as well.”

Resiliency and conventional wisdom

The study used data from the Healthy Chicago Survey, an annual survey conducted by the Chicago Department of Public Health to collect data on a range of topics, including access to health services, civic engagement, financial security, food security, mental health, neighborhood conditions, and safety. In recent years, the survey started to include questions to help measure collective efficacy in a community, such as how many neighbors people know well enough to ask for help, or their belief that they have the ability to make positive changes in their neighborhoods.

Elizabeth Tung, MD, MS

The conventional wisdom about why certain neighborhoods are more prone to gun violence is that they lack collective efficacy. Yet, the study showed that in neighborhoods that score low on collective efficacy but don’t have the same kind of poverty and other structural disadvantages, residents don’t suffer from the same rates of gun violence.

Elizabeth Tung, MD, MS, Associate Professor of Medicine and senior author of the study, says the conventional wisdom overlooks the resiliency of disadvantaged neighborhoods that manage to avoid high rates of gun violence. “The root cause is still poverty, and it's by force of nature that some communities are able to form such strong, resilient bonds to withstand structural disadvantages and economic challenges like eviction that lead to firearm violence,” she said.

Changing policies to avoid evictions

Between 2007 and 2016, more than 7,600,000 people per year faced the threat of eviction, and more than 3,600,000 were eventually forcibly removed from their housing. Black women are disproportionately impacted by eviction filings, and people who are evicted are more likely to experience financial hardship, stress, and depression. Higher eviction rates in a neighborhood are linked to low voter turnout during elections, fewer calls for city services, and even higher maternal mortality.

Statchen and Tung say it’s important to study the impact of eviction rates on gun violence because, ultimately, evictions are driven by policy choices by the state. While solving large scale poverty may seem too big of a challenge, city governments can do things to limit the number of people who are forcibly removed from their homes, like capping rent increases or improving public housing options.

“The policies that we use to govern poverty say something about what we value in society,” Tung said. “People often say there will always be poverty, but even if that’s true, we can change policies to increase the levers of opportunity and make poverty escapable rather than inescapable. Eviction is just so devastating and life changing, especially for children. So, it’s a great place to start in terms of thinking through how we handle poverty.”

The study, “Eviction, Collective Efficacy, and Firearm Violence in Chicago,” was supported by the U.S. Department of Justice, the National Institutes of Health, and the National Institute on Aging. Additional authors include Anna Volerman and Louise Hawkley from the University of Chicago.

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Journal

JAMA Network Open

DOI

10.1001/jamanetworkopen.2025.49950 

Article Title

Eviction, Collective Efficacy, and Firearm Violence in Chicago

 

Heatwaves heat up soil but not toxin levels in rice, study finds

Biochar Editorial Office, Shenyang Agricultural University

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Elevated soil temperatures during a heatwave year do not necessarily increase metal(loid) mobilization or accumulation across two harvests of semi-perennial rice: evidence from mesocosm experiments

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Credit: Qianrui Huangfu, Sha Zhang, Yuang Guo, Lu Wang, Zheng Chen, & Shuai Du

In a surprising twist amid rising climate concerns, new research shows that scorching soil temperatures during extreme heatwaves do not necessarily boost the uptake of toxic elements like arsenic in rice crops. This finding, from a real world experiment during China's record breaking 2022 heatwaves, challenges fears that global warming will poison staple foods.

"Our study reveals that soil warming alone, decoupled from air temperature rises, does not inevitably ramp up arsenic or heavy metal accumulation in rice grains," said Sha Zhang, lead researcher at the Chinese Academy of Sciences' Institute of Urban Environment and corresponding author of the paper. "This provides reassurance for food safety under future climate extremes, as plant biology and seasonal factors play bigger roles than previously thought."

Published today in Environmental and Biogeochemical Processes, the study used innovative outdoor tanks to mimic paddy fields and test soil heating from direct sunlight. Researchers grew a special type of rice called ratoon rice, which yields two harvests from one planting: a main crop and a second ratoon crop from the stubble. This setup allowed them to observe effects over an extended 143 day growing season.

The experiment took place in Suzhou, China, using large aboveground tanks filled with local paddy soil low in contaminants. Each tank had a sun exposed south side and a shaded north side, creating a natural soil warming gradient of about 5.65 degrees Celsius on average at 5 to 10 centimeters depth. Crucially, air temperatures above the plants stayed identical across sides, isolating soil effects from canopy heat stress.

Three intense heatwaves hit during the 2022 season, with air temperatures topping 36 degrees Celsius for days at a time. Soil on the warmed sides baked even hotter due to solar radiation. Despite this, porewater arsenic levels – a key measure of availability to plants – showed no significant differences between warmed and control plots in either crop (p > 0.05). While arsenic in soil water jumped tenfold from main crop (average 6.9 micrograms per liter) to ratoon crop (576.6 micrograms per liter), rice grain levels rose only modestly, from 89.8 to 123.7 micrograms per kilogram.

The team analyzed 16 elements, including toxins like arsenic, cadmium, antimony, thallium, and lead, plus nutrients such as iron, zinc, and magnesium. Warming did not spike most heavy metals in grains or porewater. Arsenic translocation from plant nodes to grains was higher in the ratoon crop, but overall accumulation stayed in check, likely due to root uptake limits early in growth.

"This decouples soil mobilization from grain contamination," noted Zheng Chen, co corresponding author at Xi'an Jiaotong Liverpool University. "Flooded conditions buffered short term heat impacts, and rice physiology acted as a natural safeguard."

Previous studies linked warming to higher arsenic via air heated setups or lab simulations, raising alarms for rice eating billions in Asia. But those often mixed soil and air effects, or ignored plant defenses like root barriers and internal storage.

Ratoon rice, popular in southern China for efficiency, faces extra scrutiny as the second crop grows in late summer heat. Yet here, soil heat did not worsen risks. Magnesium in grains even dropped on warmed plots, while other nutrients held steady.

The findings urge refined climate models distinguishing soil from air warming. "Soil heat extremes can outpace air ones, so we need field relevant tests," Zhang added. Funded by China's National Key Research Program, the work calls for multi year studies across sites.

As heatwaves intensify – with 2022's Yangtze events among the worst – this research eases some food safety worries. Rice supplies over half the calories for 3.5 billion people, and arsenic threatens health from cancer to child development.

 

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Journal reference: Huangfu Q, Zhang S, Guo Y, Wang L, Chen Z, et al. 2025. Elevated soil temperatures during a heatwave year do not necessarily increase metal(loid) mobilization or accumulation across two harvests of semi-perennial rice: evidence from mesocosm experiments. Environmental and Biogeochemical Processes 1: e017  

https://www.maxapress.com/article/doi/10.48130/ebp-0025-0017  

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About the Journal:

Environmental and Biogeochemical Processes (e-ISSN 3070-1708) is a multidisciplinary platform for communicating advances in fundamental and applied research on the interactions and processes involving the cycling of elements and compounds between the biological, geological, and chemical components of the environment. 

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DOI

10.48130/ebp-0025-0017 

Method of Research

Experimental study

Subject of Research

Not applicable

Article Title

Elevated soil temperatures during a heatwave year do not necessarily increase metal(loid) mobilization or accumulation across two harvests of semi-perennial rice: evidence from mesocosm experiments

New study uncovers how rice viruses manipulate plant defenses to protect insect vectors

Chinese Academy of Sciences Headquarters

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Proposed model illustrating how rice-infecting viruses attenuate indirect defenses against insect vectors.

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Credit: Image by ZHANG Xiaoming' Lab

Planthoppers and leafhoppers not only feed on rice plants but also act as highly efficient vectors for plant viruses, causing substantial yield losses worldwide. Notably, their persistent ability to evade natural enemies is not merely a matter of chance—it is subtly reinforced by the plant viruses they carry.

A recent study led by Prof. ZHANG Xiaoming's team at the Institute of Zoology of the Chinese Academy of Sciences (CAS), in collaboration with Prof. Ian T. Baldwin's group at the CAS Center for Excellence in Molecular Plant Sciences, has uncovered a novel ecological strategy. Rather than passively "hitchhiking" within insect vectors, rice viruses actively manipulate plant defense pathways to protect their insect carriers. This discovery reshapes our understanding of plant–virus–insect–parasitoid interactions and provides new insights for sustainable pest and pathogen management.

The findings were published in Science Advances on January 7.

Under normal conditions, rice plants respond to attacks by small brown planthoppers and other herbivorous insects by releasing methyl salicylate (MeSA), a volatile organic compound that serves as a chemical distress signal. MeSA not only deters herbivorous insects but also attracts natural enemies such as parasitoid wasps. These wasps lay their eggs inside pest eggs, effectively suppressing pest populations and forming a critical line of indirect plant defense.

However, insect-borne viruses such as Rice Stripe Virus, which is transmitted by small brown planthoppers, can disrupt this defense system. Through their NS2 protein, these viruses suppress MeSA biosynthesis and effectively silence the plant's alarm signal. As a result, parasitoid wasps are no longer recruited, and virus-carrying insects gain effective protection. This creates a self-reinforcing cycle: viruses protect their vectors and vectors in turn facilitate viral transmission.

To break this cycle, the researchers conducted large-scale field experiments over two consecutive years in Jurong, Jiangsu Province. By deploying slow-release MeSA dispensers in rice paddies, they restored the disrupted plant signaling. The results showed that parasitoid wasp abundance increased significantly, pest populations declined, and egg parasitism rates rose from approximately 40% in virus-infected fields to over 60%—matching levels observed in virus-free fields. Meanwhile, viral transmission was effectively suppressed.

As MeSA is a natural metabolite produced by rice plants, this strategy is environmentally friendly, free of chemical pollution, and unlikely to induce resistance. Instead of eliminating pests outright, it restores disrupted ecological interactions and reactivates nature's inherent pest control mechanisms.

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Journal

Science Advances

DOI

10.1126/sciadv.aeb5215