Infant Microbiome Atlas Makes Case for Region-Specific Probiotics
By Deborah Borfitz
March 5, 2026 | When it comes to the microbiome, “our bodies are beautifully designed for a world that no longer exists,” according to Trevor Lawley, Ph.D., senior group leader of the Host-Microbiota Interactions Lab at the Wellcome Sanger Institute (U.K.). The bugs inhabiting our gut are a good match for high-fiber, plant-based dietary habits that have been largely replaced by processed foods that are killing off health-promoting bacteria and allowing more harmful varieties to dominate.
Probiotics currently on the market and claiming to remedy the situation in babies are in fact missing many of the beneficial microbes, he adds. They are also not formulated with bacterial strains found naturally in different regions and aligned with local culinary traditions.
These are among the conclusions drawn from a global atlas mapping two key gut bacteria in infants around the world, which was published recently in Cell (DOI: 10.1016/j.cell.2026.01.007). It lays the foundation for “geographic-specific” probiotics that are more effective—most importantly, with the crucial, rapidly disappearing, and often mislabeled Bifidobacterium infantis strain.
The key infant-gut species is largely absent among babies in Western countries in Europe and North America, but highly common in infants born in African and South Asian countries. Every commercial infant probiotic is “basically isolated from one child from Germany in 1940,” says Lawley. Except for a couple of genetic tweaks, the products are identical in terms of their clonal lineage even if they’re marketed under different strain names.
B. infantis strains naturally residing in the infant gut are adapted to local diets and components in breast milk, he adds. These include urea, which helps establish a healthy digestive system for infants, and B vitamins that are important for their neural development.
One of the most conserved gene clusters break down urea, and the hypothesis is that they’re using nitrogen to produce amino acids to feed muscle growth in babies, says Lawley. B. infantis is highly adapted to feeding off urea and, without it, will disappear, he adds, pointing to the impact of diet on the composition and assembly of the microbiome.
‘Bugs as Drugs’
The bulk of Lawley’s career making “bugs as drugs” has been at the Wellcome Sanger Institute. His early work revolved around finding an alternative to fecal transplants for Clostridioides difficile, the notorious bacterium causing severe, often antibiotic-associated diarrhea and colitis. After the patents began piling up, he co-founded Microbiotica in 2016, where the focus has been on inflammatory bowel disease and cancer.
Lawley serves as chief scientific officer of the biotech company, a spinout from the Host-Microbiota Interactions Laboratory, which recently announced the success of a phase 1b trial of a live biotherapeutic product (LBP) for ulcerative colitis (UC). Unlike commercial probiotics, LBPs are regulated as pharmaceutical drugs to treat or prevent specific diseases rather than marketed as dietary supplements.
LBPs contain live microorganisms like Bifidobacterium and have been used to reduce the incidence of necrotizing enterocolitis (NEC) and allergies in babies known or suspected to have an unhealthy imbalance of microbes in their gut, often triggered by C-sections or antibiotic use, says Lawley. Siolta Therapeutics, a leader in the baby LBP space, released its phase 2 data late last year on its oral microbial therapy to prevent atopic dermatitis.
A phase 2 study for the LBP designed to treat UC in adults is the next step for Microbiotica, Lawley says. The company’s forte is in using genomics to identify strains and pair them with clinical phenotypes to develop precision medicines. The challenge here is sorting out the function and impact of hundreds of gut microbes that are interacting and supporting and competing with one another.
Microbiotica has already significantly advanced the manufacturing of anaerobic gut microbes for therapeutic use, he adds. “It’s a completely new type of medicine and ... we’re going to be the gold standard” for how to identify and make the strains.
While the Food and Drug Administration (FDA) has to date approved two LBPs, both for the prevention of recurrence of C. difficile infection in adults, the agency has not approved any probiotic product as a drug or biological product for people of any age. In fact, the FDA issued warning letters to two companies in 2023 for illegally selling probiotic products used to treat diseases in preterm infants.
“There were some bacteremia and deaths in premature babies and that’s a huge red flag,” says Lawley, although there are also “clear health benefits to giving these probiotics to infants. “We’re hoping our paper can provide some way to move forward in terms of resources and strains.”
It’s also possible that reducing the dose of probiotics, and the frequency of administration, might help eliminate any risks, he adds. Babies are being given massive doses, and “you don’t need a lot to get them colonized.”
Evidence is being built by companies, including Persephone, that babies need their microbiomes supplemented with Bifidobacteria to train their immune system for life. The most recent study by
Persephone highlights the essential role of key Bifidobacterium species in early-life immune development and long-term health (Cell Host & Microbe, DOI: 10.1016/j.chom.2025.10.017).
But, as Lawley’s latest study suggests, current approaches to developing infant probiotics may need some serious revisions.
It is going to “challenge the probiotic industry ... with science,” he says, “which has been a long time coming.” Manufacturers, distributors, and marketers may be reluctant to cultivate new geographic-specific strains because it will mean much more upfront investment to ensure they remain alive and viable until consumed and effectively colonize the gut.
Benefits of Bacteria
Africa is the “ancestral home” of the microbiome, but since World War II many big societal changes have occurred, among them smaller family sizes, the mass production of antibiotics, formula milk as a cultural norm in Western nations, and surging popularity of processed foods, says Lawley. They have collectively transformed the body’s relationship with microbes, with some of the bugs thought to be vital to human health disappearing.
B. infantis, which Lawley calls “the coolest bug I have worked on my whole career,” is but one of them. It’s the now-missing link between moms, babies, and the metabolites in nutrient- and energy-producing breast milk.
Next-generation sequencing reveals the benefit of these bacteria, he points out. They make a lot of B vitamins, for example, notably B9 (folic acid) important for neural development that most pregnant women take as supplements. They also help with the processing of sphingolipids, which are essential structural and signaling lipids in baby neuron membranes.
Missingness of these beneficial bacteria could be one possible explanation for the rise of chronic diseases in the westernized world, says Lawley. Individuals born by Cesarean section are at significantly higher risk of developing metabolic syndromes such as obesity as well as autoimmune conditions, neurodevelopmental issues, and cognition problems once they start going to school.
The newly created global atlas highlights previously unknown diversity in B. infantis and identifies 36 related strains of bacteria, or clades, which are tied to certain geographic regions, Lawley reports. He and his colleagues found four big groups representing the westernized world (Europe and North America), West Africa, East Africa, and Asia.
Specialization also exists within each of those regions, he adds. Changes between the different clades in different parts of the world often reflect the bacteria adapting to local diets, which in East and West Africa are non-industrialized, grain-based foods enriched in region-specific micronutrients. “We can look at the genomes of these bugs from each region and predict what the local diet is to some degree.”
Ecological Succcession
Diets likely have a determining effect on the population of bugs in the gut throughout life. “Babies are born with no microbiome; they come out of the mom sterile, and then ecological succession starts happening,” says Lawley. “The first bug there has the advantage and they can exclude bugs or they can let bugs in.”
In his lectures, Lawley often depicts this “priority effects” phenomenon with a side-by-side view of the lush Azores, in Portugal, and Lanzarote, an arid Spanish island in the Atlantic Ocean near Africa that emerged due to volcanic activity 15 million years ago. “They’re being seeded by different forms of life and that’s what happens to babies,” he says. “And these ecological successions are to some degree quite predictable.”
The way a baby’s microbiome gets assembled has parallels to the way volcanic islands get seeded, says Lawley, referencing a 2024 paper identifying the crucial role played by Bifidobacteria in shaping the microbiota assembly and functions in early life (Nature Microbiology, DOI: 10.1038/s41564-024-01804-9). The study looked at about 1,300 U.K. babies in the first few weeks of life and found one of three types of ecosystems formed in their guts, two of them dominated by the presumably beneficial bacteria (B. longum and B. breve) and a third by Enterococcus faecalis associated with persistent high pathogen loads and originating in the healthcare environment—generally to babies born by Cesarean section.
“Breast milk is the most amazing food there is and ... you can’t replace that with formula milk,” he continues. Infant formula contains “just a few” of the same vital ingredients as what nature provides.
Beyond suboptimal formula feeding, antibiotics represent an additional, and “very destructive” seeding event.
It’s the same sort of story with adults who subsist on ultra-processed foods, he says, citing soda pop and high-sugar candies. “I think some of those products should have comparable [health] warnings as cigarettes. They’re that damaging to the microbiome ... supporting the growth of non-ideal bugs and starving the good bugs.”
Geography Matters
Before the global atlas was created, it was uncertain if B. infantis and B. longum were two separate species or one in the same. The reason, says Lawley, is simple: all the sampling was being done in North America and Europe.
He and his team have instead sequenced a lot of samples from Africa where the bugs weren’t going extinct. This gave them the ability to confidently say that B. infantis and B. longum are different species that co-evolved from a common ancestor. In westernized babies, however, “infantis is disappearing but longum is coming in and taking its place,” he says.
“We don’t know if that’s bad, but it’s not ideal,” Lawley adds. After examining the data, “you would have to wonder if there is a detrimental impact on the child.”
Elective C-sections are life-saving clinical procedures that are underused in certain parts of the world, especially in Sub-Saharan Africa, he says. But in places like America and the U.K., the C-section rate is upwards of 25% and, in Columbia, around 60%—well above the ideal 10% to 15% population-level rate traditionally cited by the World Health Organization.
That B. longum is replacing B. infantis is the westernized world is additionally concerning, because longum can’t use components of breast milk, such as urea and good sugars, continues Lawley. “If there are health benefits [to urea], longum can’t metabolize and break it down, so there are opportunities lost there.”
On the other hand, “I would rather have longum than Enterococcus faecalis.” In a 2025 study in the U.K. birth cohort, he and his collaborators found an association between the gut bacterium in infants and subsequent viral respiratory infections during their first two years of life, while B. longum was found to have a protective effect (The Lancet Microbe, DOI: 10.1016/S2666-5247(22)00184-7).
Data-Sharing Woes
A major part of the work currently being done in the Host-Microbiota Interactions Lab at Sanger is next-generation sequencing of baby microbiomes from 20 nations around the world, as well as training up students from each of those geographies to establish labs for the same type of work in their home country, says Lawley. “I have three Kenyans in the lab now, and we recently had someone from Bangladesh and someone from Uganda. It has had a huge positive impact on my lab.”
To help fill the gaps in publicly available microbiome profiles from infants outside North America and Europe, Lawley was part of the ongoing Childhood Acute Illness and Nutrition Network (CHAIN) study endeavoring to identify the biological mechanisms and socioeconomic factors that determine a child’s risk of mortality. It provided some of the data used in the latest Cell paper.
The CHAIN study currently encompasses 12,000 gut metagenomes from about 4,000 babies, from longitudinal sampling being done in sub-Saharan Africa and South Asia.
Well over 100 countries, including all the European Union plus the U.K., have ratified the Nagoya Protocol intended to ensure fair access and benefit-sharing of genetic resources, which now includes the newly compiled global atlas of the infant gut microbiome. While the principle is noble, “the implementation has been a disaster,” says Lawley. This has created “hidden invisible barriers” to synchronization. “We’re still trying to figure out how to navigate for some countries.”
In the meantime, “take good care of your microbiome,” he advises. It’s a functional, supporting organ which, if abused, is going to become severely depleted and lead to potentially lasting harms.