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

 

Portable biosensor may enable on-site PFAS detection

La Trobe University

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A portable biosensor developed at La Trobe University may allow rapid, on-site detection of toxic “forever chemicals” in water, removing the need for samples to be sent to specialist laboratories.

The device is designed to detect per- and polyfluoroalkyl substances (PFAS), a group of more than 15,000 synthetic chemicals used in products such as firefighting foams, food packaging and stain-resistant fabrics.

PFAS are highly persistent in the environment and have been linked to serious health risks, including cancer. Specifically, the sensing device detects PFOA (perfluorooctanoic acid), which is among the most regulated PFAS.

Led by PhD student Henry Bellette and Dr Saimon Moraes Silva, Director of La Trobe’s Biomedical and Environmental Sensor Technology (BEST) Research Centre, the research has been published in the journal ACS Sensors.

Bellette said current PFAS-testing methods limited how often and where water could be monitored.

“Most PFAS testing relies on expensive laboratory equipment and specialist analysis, which makes regular monitoring difficult,” he said. “This biosensor could be used on site and provides a simple yes or no result, allowing water to be screened quickly and easily.”

PFAS contamination has been identified across Australia, particularly at sites where firefighting foams were historically used, including airports, military bases and fire stations.

Dr Moraes Silva said portable screening tools would play an important role in managing long - term contamination.

“PFAS do not break down in the environment, so monitoring is an ongoing challenge,” he said. “A portable screening tool could allow more frequent testing, particularly in regional and remote areas, and help identify where more detailed laboratory analysis is needed.”

The researchers hope the technology can eventually be incorporated into a hand -held device for environmental monitoring and water screening.

DOI: https://doi.org/10.1021/acssensors.5c03678

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Journal

ACS Sensors

DOI

10.1021/acssensors.5c03678 

Method of Research

Experimental study

Subject of Research

Not applicable

Article Title

Point-of-Need PFAS Detection: A Yes/No Biosensor SolutionArticle link copied!

‘Forever chemicals’ may increase liver disease risk in adolescents by as much as 3-fold

A research collaboration co-led by USC and the University of Hawai’i found that higher levels of two common types of PFAS in the blood were linked to an increased risk of early onset of MASLD, formerly known as fatty liver disease.

Keck School of Medicine of USC

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A new study co-led by the Southern California Superfund Research and Training Program for PFAS Assessment, Remediation and Prevention (ShARP) Center and the University of Hawai‘i has linked certain common “forever chemicals” to a higher risk of liver disease in adolescents. These synthetic compounds, known as per- and polyfluoroalkyl substances (PFAS), may as much as triple the chances that adolescents develop a liver condition called metabolic dysfunction-associated steatotic liver disease (MASLD) — formerly known as fatty liver disease. 

The findings were published in the journal Environmental Research.

MASLD affects about 10% of children and up to 40% of children with obesity. It is a chronic condition that doesn’t always have telltale symptoms, although some patients experience fatigue, discomfort and abdominal pain. The disease increases long-term risk for type 2 diabetes, heart disease, advanced liver injury, cirrhosis and even liver cancer. 

“MASLD can progress silently for years before causing serious health problems,” said Lida Chatzi, MD, PhD, a professor of population and public health sciences and pediatrics and the director of the ShARP Center, a national center funded by the National Institute of Environmental Health Sciences to investigate PFAS health impacts, advance cleanup technologies and support affected communities. “When liver fat starts accumulating in adolescence, it may set the stage for a lifetime of metabolic and liver health challenges. If we reduce PFAS exposure early, we may help prevent liver disease later. That’s a powerful public-health opportunity.”

PFAS are manufactured chemicals used in nonstick cookware, stain- and water-repellent fabrics, food packaging and some cleaning products. They persist in the environment and accumulate in the body over time. More than 99% of people in the U.S. have measurable PFAS in their blood, and at least one PFAS is present in roughly half of U.S. drinking water supplies.

“Adolescents are particularly more vulnerable to the health effects of PFAS as it is a critical period of development and growth,” said the study’s first and corresponding author Shiwen “Sherlock” Li, PhD, an assistant professor of public health sciences at the University of Hawai‘i. “In addition to liver disease, PFAS exposure has been associated with a range of adverse health outcomes, including several types of cancer.”

Linking PFAS, genetics, and lifestyle

The research examined 284 Southern California adolescents and young adults from two USC longitudinal studies. The participants were already at higher metabolic risk because their parents had type 2 diabetes or were overweight. PFAS levels were measured through blood tests, and liver fat was assessed using MRI.

Higher blood levels of two common PFAS — perfluorooctanoic acid (PFOA) and perfluoroheptanoic acid (PFHpA) — were linked to a greater likelihood of MASLD. Adolescents with twice as much PFOA in their blood were nearly three times more likely to have MASLD. The risk was even higher for those with a genetic variant (PNPLA3 GG) known to influence liver fat. In young adults, smoking further amplified PFAS-related liver impacts.

“These findings suggest that PFAS exposures, genetics and lifestyle factors work together to influence who has greater risk of developing MASLD as a function of your life stage,” said Max Aung, PhD, MPH, assistant professor of population and public health sciences at the Keck School of Medicine. “Understanding gene and environment interactions can help advance precision environmental health for MASLD.”

Li noted that this study is the first to examine PFAS and MASLD in children using gold-standard diagnostic criteria, and the first to explore how genetic and lifestyle factors may interact with PFAS exposure. MASLD also became more common as adolescents grew older, adding to evidence that puberty and early adulthood may increase susceptibility to environmental exposures.

The study builds on recent USC research showing that, for adolescents undergoing bariatric surgery to manage obesity, a PFAS known as PFHpA is linked to more severe liver disease, including inflammation and scarring of connective tissue called fibrosis. 

“Taken together, the two studies show that PFAS exposures not only disrupt liver biology but also translate into real liver disease risk in youth,” Chatzi said. “Adolescence seems to be a critical window of susceptibility, suggesting PFAS exposure may matter most when the liver is still developing.”

About this study

Other co-authors are Jiawen Carmen Chen, Jesse Goodrich, Lily Dara, Lucy Golden-Mason, Ana Maretti-Mira, Zhanghua Chen, Frank Gilliland, Brittney Baumert, Sarah Rock, Sandrah Eckel, David Conti and Rob McConnell, all of USC; Elizabeth Costello, who is affiliated with USC and Brown University; Douglas Walker of Emory University; Scott Bartell and Veronica Vieira of UC Irvine; Tanya Alderete of Johns Hopkins University; Michael Goran of Children’s Hospital Los Angeles; and Alan Ducatman of West Virginia University.

The study was funded by the National Institutes of Health [P42ES036506, R01DK59211, 5P01ES022845-03, 5P30ES007048, 5P01ES011627, R01/ES029944, R01ES030691, R01ES030364, R01ES033688, U01HG013288, R01ES035035, R01ES035056, P50MD17344, T32-ES013678, ES035035], the U.S. Environmental Protection Agency [RD83544101] and the Hastings Foundation. 

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Journal

Environmental Research

DOI

10.1016/j.envres.2025.123320 

Method of Research

Data/statistical analysis

Subject of Research

People

Article Title

Associations between per- and polyfluoroalkyl substances and metabolic dysfunction-associated steatotic liver disease in adolescents and young adults: modifying roles of age, lifestyle factors, and PNPLA3 genotype

Article Publication Date

12-Nov-2025

COI Statement

The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Dr Chatzi and Dr Ducatman have served as an expert consultants for plaintiffs in litigation related to PFAS-contaminated drinking water.

French ban on ‘forever chemicals' in cosmetics and clothes to enter into force

A French ban on the production and sale of PFAS chemicals – known as 'forever chemicals' as it takes them so long to break down – comes into effect on Thursday. The ban targets a wide range of cosmetics and clothes and will also require French authorities to regularly test drinking water for all kinds of PFAS.


Issued on: 30/12/2025 
By: FRANCE 24

The French cosmetics industry is worth over €30 billion per year, according to the French association of beauty companies FEBEA. © Alain Jocard, AFP

A French ban on the production and sale of cosmetics and most clothing containing polluting and health-threatening "forever chemicals" goes into force on Thursday.

Per- and polyfluoroalkyl substances (PFAS) are human-made chemicals used since the late 1940s to mass produce the non-stick, waterproof and stain-resistant treatments that coat everything from frying pans to umbrellas, carpets and dental floss.

Because PFAS take an extremely long time to break down – earning them their "forever" nickname – they have seeped into the soil and groundwater, and from there into the food chain and drinking water.

These chemicals have been detected virtually everywhere on Earth, from the top of Mount Everest to inside human blood and brains.


Chronic exposure to even low levels of the chemicals has been linked to liver damage, high cholesterol, reduced immune responses, low birthweights and several kinds of cancer.

The French law, approved by lawmakers in February, bans the production, import or sale from January 2026 of any product for which an alternative to PFAS already exists.

These include cosmetics and ski wax, as well as clothing containing the chemicals, except certain "essential" industrial textiles.

A ban on non-stick saucepans was removed from the draft law after intense lobbying from the owners of French manufacturer Tefal.

It will also make French authorities regularly test drinking water for all kinds of PFAS.

READ MOREFrench food safety agency finds forever chemicals in more than 90% of tap water

There are thousands of different PFAS and certain ones have been banned since 2019 under the Stockholm Convention on Persistent Organic Pollutants, but China and the United States are not among the more than 150 signatories.

This includes perfluorooctanoic acid (PFOA), used since the 1950s by US company DuPont to manufacture its non-stick Teflon coating for textiles and other everyday consumer products.

The Stockholm Convention also bans perfluorooctane sulfonic acid (PFOS), known for its use as a waterproofing agent by the US group 3M, which has been heavily restricted since 2009.

A handful of US states, including California, implemented a ban on the intentional use of PFAS in cosmetics beginning in 2025, and several other states are slated to follow in 2026.

Denmark will ban the use of PFAS in clothing, footwear and certain consumer products with waterproofing agents beginning on July 1, 2026.

Denmark has banned the use of PFAS in food packaging since 2020.

The European Union has been studying a possible ban on the use of PFAS in consumer products, but has not yet presented or implemented such a regulation.

(FRANCE 24 with AFP)

 

CityUHK scholar participates in global study revealing global food‑safety risks in marine fish

Some local fish species found with higher levels of toxic compounds

Communications and Institutional Research Office, City University of Hong Kong

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CityUHK researchers identified the above four local fish species with relatively high PFAS levels.

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Credit: City University of Hong Kong

A research team from City University of Hong Kong (CityUHK) recently collaborated with an international research team to publish a study revealing a correlation between global contamination of per- and polyfluoroalkyl substances (PFAS) in globally consumed edible marine fish and associated human health risks.

The study found that consumers may be exposed to elevated levels of PFAS by consuming imported fish such as salmon, tuna, swordfish and cod — even in regions with low environmental pollution — thereby increasing food‑safety risks.

The research was jointly led by Professor Qiu Wenhui and Professor Zheng Chunmiao, from the School of Environmental Science and Engineering at Southern University of Science and Technology in the Chinese Mainland. Professor Kenneth Leung Mei-yee, Director of the State Key Laboratory of Marine Environmental Health, Chair Professor of the Department of Chemistry and Associate Dean of the College of Science at CityUHK, served as a co‑author of the study. The findings were recently published in the international journal Science, under the title “Risks of Per- and Polyfluoroalkyl Substance Exposure through Marine Fish Consumption”.

The team compiled seawater‑monitoring data from 3,126 locations worldwide over the past 20 years and used marine food‑web models to analyse PFAS concentrations in 212 edible marine fish species. They found that PFAS levels are closely linked to the pollution history and dilution capacity of marine regions, with significantly higher concentrations found in predatory species at high trophic levels.

PFAS are synthetic chemicals widely used in industrial and consumer products, such as non‑stick cookware, waterproof clothing and firefighting foams. Owing to their extreme chemical stability, PFAS are slow to degrade in the natural environment and tend to accumulate in organisms and move up the food chain, posing potential risks to human health.

The study’s findings reveal that between 2010 and 2021, the median concentration of C8‑PFAS — including PFOA and PFOS — in global marine fish was 0.34 ng/g wet weight. In Asia, the median level was notably higher than that in other regions, reaching 1.03 ng/g wet weight. Some marine fish species from Saudi Arabia and Thailand exhibited even higher contamination levels at 11.72 and 6.06 ng/g wet weight, respectively.

The team also analysed fisheries and trade data from 33 countries, along with estimated daily intake (EDI) levels of various fish species. They found that high-risk contaminated species, such as cod, herring, sea bass, salmon, tuna and swordfish, are sourced mainly from Europe and traded to other markets. This indicates that consumers in local sea areas with low contamination levels may still be exposed to higher food-safety risks because of imported fish, leading to a “cross‑border transfer” of PFAS exposure. For example, in Italy, only 11.71% of fish is imported from Sweden, but these imports account for 35.82% of Italians’ C8‑PFAS intake. In contrast, the domestic fish catch in Italy accounts for 28.02% of consumption but only 5.23% of C8-PFAS exposure. Similar patters were observed in the United Kingdom and Colombia.

Professor Leung and his research team at CityUHK, including Professor Ruan Yufei, Assistant Professor in the Department of Chemistry, and Dr Qi Wang, postdoctoral fellow, also conducted tests on PFAS contamination in local fish species commonly caught in Hong Kong waters.

The results indicate that while overall PFAS exposure risks from local fish remained low in Hong Kong, several species were found to contain relatively high PFAS concentrations, including Blackspot threadfin (Polydactylus sextarius), Daggertooth pike conger (Muraenesox cinereus), Indian thryssa (Thryssa kammalensis) and Burrowing goby (Trypauchen vagina).

Professor Leung noted that three categories of fish tend to pose higher PFAS‑exposure risks:

• Predatory species at high trophic levels, such as threadfin, conger, cod, tuna and swordfish;
• High‑fat species, such as salmon, herring and sardines; and
• Demersal (bottom‑dwelling) species, such as the burrowing goby.

“Elderly people, pregnant women, young children and individuals with chronic illnesses are more vulnerable to PFAS‑related risks and should therefore be especially careful when choosing seafood,” said Professor Leung. “The public is also advised to maintain a balanced diet and limit their consumption of fish species known to have elevated PFAS levels to minimise potential health risks.”

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Journal

Science

DOI

10.1126/science.adr0351 

Method of Research

Experimental study

Subject of Research

Animals

Article Title

Risks of per- and polyfluoroalkyl substance exposure through marine fish consumption