Bifidobacteria are predominantly found in the gut of newborn children. These bacteria are probiotic and help the immune system develop, reduce inflammation and protect against sickness.
In the adult stage, these bacteria continue to support digestion and immunity. They also help develop a healthy community of gut bacteria to strengthen bones, promote heart health, and boost mental well-being.
However, probiotic products containing Bifidobacterium do not always work the same way for everyone. They work well for some and not so well for others. Scientists suspect that this variation comes from differences in each person’s existing gut bacteria.
How does the composition and functional potential of individual baseline gut microbiome influence the colonization and persistence of Bifidobacterium probiotics?
Researchers from IIIT-Delhi and AIIMS Delhi collaborated with researchers in Ireland to analyse the gut microbiota composition of over 50,000 people across 149 study groups, from around 45 countries around the world. They grouped people by age and lifestyle, as well as by sequencing methods used for identifying the gut microbes.
The results showed that age and lifestyle made a difference in gut microbiome composition. In most study groups, the other bacteria present in the gut influenced the levels of the Bifidobacteria. This connection was strongest in babies and gradually decreased with age.
There are so many different bacterial species in the gut. Which bacteria most influence the variations in the levels of Bifidobacteria?
To narrow down which specific bacteria or microbiome properties in general were the top predictors for Bifidobacterium,the researchers built a machine learning model based approach stratified by the location, life-style and age of the individuals (or cohort-types).
The model identified butyrate-producing Firmicutes and Collinsella as common predictors across different cohort types.
How can we measure the strengths of such relationships between gut microbes?
The researchers created association-scores to measure how helpful or harmful a specific gut bacterium is to a specific Bifidobacterium. Butyrate producing bacteria and Collinsella were strongly linked to Bifidobacterium adolescentis, and Bifidobacterium longum. Disease linked bacteria were associated with B. breve and B. dentium.
Some of these associations may be due to factors such as diet or medications. So, the researchers checked the association-scores mathematically by adjusting the effect of diet, medication and host clinical markers.
The scores revealed that butyrate-producing Firmicutes and bacteria from the genus Collinsella are friendly to Bifidobacteria. But some other species of Firmicutes and specific Bacteroidota taxa are unfriendly to Bifidobacteria. These patterns remained stable even when individuals had cancer, diabetes, heart disease, COVID or Parkinson’s.
How can these findings be used by doctors to predict a patient’s response to a probiotic even before they start treatment?
The researchers introduced a new concept: receptive-score. The score ranks a person’s gut in two ways — how supportive the other bacteria are, and how much of the target probiotic is already there in the gut. The researchers tested the concept across eight clinical trials. The receptive-score correctly predicted probiotic success most of the time. Higher scores were also linked to better health outcomes, such as reduced diarrhoea and inflammation.
But how do these bacteria help or hurt the Bifidobacteria?
The researchers analysed the genomes of 66 bacteria to find genes linked to their association-scores. This helped them understand how friendly bacteria help probiotics grow by sharing sugars.
“We identified 162 Bifidobacterium-derived functional genetic traits linked to the success of Bifidobacterium establishing itself as a probiotic in the gut. Positive associations were linked to sugar transport and fatty acid production, while negative associations were linked to metal ion transport”, says Alisha Ansari, IIIT Delhi.
“The successful colonisation of Bifidobacterium probiotics is not random. It depends on which other bacteria are already living in your gut”, adds Sourav Goswami, IIIT Delhi.
By analysing a very large dataset of microbiomes, the researchers identified consistent taxonomic and functional rules that determine whether a probiotic will stay and grow.
“In practical terms, this work is a very preliminary step toward gut tests that could one day help predict whether a given probiotic is likely to take hold in a particular person, before they try it”, says Tarini Shankar Ghosh, IIIT Delhi.
Nature Communications, 17: 5678 (2026);
DOI: 10.1038/s41467-026-72289-9
Reported by S Gayathri with inputs from Aritha Chandrasekhar,
PhD scholars working with A Satya, Sastra Deemed University, Thanjavur
This report was written during a workshop
for capacity building of Indian PhD scholars
organised and conducted by scienceandmediaworkshops
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