You said my microbiome is changing how?
You said my microbiome is changing how?

Changes in poop quantity, quality, and color is a concern to gut microbiome scientists and parents alike. In Science of Mom’s recent post “How Often Should a Baby Poop?” she discusses the amazing variability in pooping patterns between babies and also as a kid ages. I was, of course, excited to see that she mentioned a little about the influence of the gut microbiome, but her post inspired me to think more about pooping patterns from a microbiome perspective.

Individual variability

First, it’s not too surprising that there’s a huge variability between infants and pooping frequency. Several studies demonstrate that each individual’s gut microbiome is unique. In the guts of healthy adults, a single, unique bacterial strain can be used to identify each individual [1]. With each bacterial strain comes some unique abilities. Various bacterial taxa digest different foods and/or produce and transport different vitamins, amino acids, and other basic nutrients. So microbiome community A may process the nutrients faster, more efficiently, or completely than microbiome community B. That difference in the microbiome community function plus the differences in human gut anatomy due to human genetics could lead to a wide range in pooping frequency.

Feeding differences

Second, as Science of Mom mentions, exclusively breast-fed infants have a different microbiome, with fewer types of bacteria than formula fed babies. The microbiome differs due to the prebiotic sugars present in breast milk that are not digested by the infant, but instead by the infant’s gut microbiome. Specifically the Bfidobacterium species [2-5]. In contrast, formula has different types and ratios of sugars than breast milk that a diversity of bacteria can feed upon. How well and how quickly the formula-feeding bacteria digest the compounds in formula may explain why formula takes longer to digest than breast milk. Certainly, poop rate and consistency differs between formula and breast milk-fed babies!MicrobirthBreastvBottle5nocaption

Even within breast-fed babies, there is a great deal of poop variation. Such fluctuations in poop could be due to how the microbiome responds to the changing composition of breast milk, especially the prebiotic sugars, across time. Which and how much of these prebiotic sugars are present varies during a feeding session (between fore and hind milk), during a day, across infant development, and between mothers [6-9]. The difference between mothers is partially due to mom’s genetics [10], but may also depend on the microbiome present in the infant and perhaps also in the mother. How does a mother’s digestive system and breast milk microbiome influence milk composition? How does mom’s diet influence breast milk composition? Then, how do these changes in sugar and other compounds in breast milk influences microbe numbers and diversity, much less gut transit time?

Third, the introduction of solid food anywhere from 4 to 6 months of age certainly changes what transits the baby’s gut. From a microbiome perspective, with the introduction of solid foods comes an increase in the types of bacteria. Some of the increase in bacterial diversity may come into the gut with the solid foods [11] or other goodies (intended or not!) that get into infant’s mouths. However, many of them were instead acquired during birth from mom. These bacteria are often few in number and “hide in the wings” during breast milk or formula feeding until the appropriate solid food source is eaten. A recent paper suggests that actually it’s not the introduction of solid food that changes the microbiome diversity, but instead it’s the cessation of breast-feeding [12]. Interesting to consider.

Personal Poop

Certainly as a mother of two girls (2 and 7 years old), I’ve experienced these different stages and transitions. Both girls were exclusively breast-fed until ~ 7 months. Jac, the oldest, had antibiotics at 6 months old, so I delayed starting solid food until about 3 weeks after she finished the last dose of antibiotics. Though, to date, no studies that I am aware of have studied the influence of breastfeeding on the infant microbiome after antibiotics. At that time – a whole 6 years ago – we knew that antibiotic significantly influenced the gut microbiome and that breastfeeding was important for initial establishment – somehow. The genome paper suggesting that Bfidobacterium longum subsp. infantis actually breaks down breast milk sugars [13] was published when Jac took that first dose of antibiotics! Did the breastfeeding help to restore her microbiome? I’m not sure, but I doubt it hurt.

Emily just turned 2 and is showing no sign of stopping breast-feeding. Much more so than her older sister at this same age. However, unlike her sister at that age, Emily is a pooper. Goodness. We change 3-5 poopy diapers a day. Is this because her microbiome is more similar to a breast-fed infant’s microbiome, as seen in the Bäckhed, et al. 2015 paper? Perhaps it’s the amount of beans that child eats. She loves her beans!! In contrast, Jac at 2 years was breast-feeding only once at night and started getting constipated. So much so that the pediatrician we had at the time suggested a laxative that contains polyethylene glycol, an emulsifier. If I’d known then what I know now we would have found a different alternative, but that’s a post for another day. Ironically, I never fed either one of them rice cereal due to concerns about the potential for constipation, but started with veggies, fruits, and oatmeal.

Finally, a commenter, Anya, on the site asked about eczema and transit time. While I haven’t found much on this, one thing we do know is that babies with eczema/atopic dermatitis have a very different microbiome than infants without eczema. Whether the different microbiome community is in response to the eczema or causes it is unknown [14-16].

It’s amazing to think of how quickly the study of the human microbiome has developed in the 7 years that I’ve been a mama. I’m sure with many more dirty diapers, poop filled microfuge tubes, and many more billions of microbiome sequences we’ll learn even more. Perhaps when my girls are old enough to have kids, pediatricians will no longer prescribe emulsifiers as laxatives. Instead, they will swab a bit of the poopy diaper on a sensor and get a bacterial or food “prescription” to change the gut microbiome. If so, those are some diapers I’m really looking forward to changing!

If you have a question about poop or the microbiome – feel free to ask. All crappy questions are welcome below (sorry – I couldn’t resist).



  1. Eloe-Fadrosh, E. A., A. Brady, J. Crabtree, E. F. Drabek, B. Ma, A. Mahurkar, J. Ravel, M. Haverkamp, A.-M. Fiorino, C. Botelho, et al. 2015. Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption. mBio 6.
  2. Guaraldi, F., and G. Salvatori. 2012. Effect of Breast and Formula Feeding on Gut Microbiota Shaping in Newborns. Frontiers in Cellular and Infection Microbiology 2:94.
  3. Azad, M. B., T. Konya, H. Maughan, D. S. Guttman, C. J. Field, R. S. Chari, M. R. Sears, A. B. Becker, J. A. Scott, and A. L. Kozyrskyj. 2013. Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months. Canadian Medical Association Journal 185:385-394.
  4. Jost, T., C. Lacroix, C. Braegger, and C. Chassard. 2015. Impact of human milk bacteria and oligosaccharides on neonatal gut microbiota establishment and gut health, vol.
  5. Mueller, N. T., E. Bakacs, J. Combellick, Z. Grigoryan, and M. G. Dominguez-Bello. 2015. The infant microbiome development: mom matters. Trends in Molecular Medicine 21:109-117.
  6. Kunz, C., S. Rudloff, W. Baier, N. Klein, and S. Strobel. 2000. Oligosaccharides in Human Milk: Structural, Functional, and Metabolic Aspects. Annual Review of Nutrition 20:699-722.
  7. Allen-Blevins, C. R., D. A. Sela, and K. Hinde. 2015. Milk Bioactives May Manipulate Microbes to Mediate Parent-Offspring Conflict. Evolution, Medicine, and Public Health.
  8. Petherick, A. 2010. Development: Mother’s milk: A rich opportunity. Nature 468:S5-S7.
  9. Ballard, O., and A. L. Morrow. 2013. Human Milk Composition: Nutrients and Bioactive Factors. Pediatric clinics of North America 60:49-74.
  10. Lewis, Z., S. Totten, J. Smilowitz, M. Popovic, E. Parker, D. Lemay, M. Van Tassell, M. Miller, Y.-S. Jin, J. German, et al. 2015. Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants. Microbiome 3:13.
  11. Graf, D., R. Di Cagno, F. Fåk, H. J. Flint, M. Nyman, M. Saarela, and B. Watzl. 2015. Contribution of diet to the composition of the human gut microbiota. 2015 26.
  12. Bäckhed, F., J. Roswall, Y. Peng, Q. Feng, H. Jia, P. Kovatcheva-Datchary, Y. Li, Y. Xia, H. Xie, H. Zhong, et al. 2015. Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. Cell Host & Microbe 17:690-703.
  13. Sela, D. A., J. Chapman, A. Adeuya, J. H. Kim, F. Chen, T. R. Whitehead, A. Lapidus, D. S. Rokhsar, C. B. Lebrilla, J. B. German, et al. 2008. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proceedings of the National Academy of Sciences 105:18964-18969.
  14. Kobayashi, T., M. Glatz, K. Horiuchi, H. Kawasaki, H. Akiyama, Daniel H. Kaplan, Heidi H. Kong, M. Amagai, and K. Nagao. 2015. Dysbiosis and Staphyloccus aureus Colonization Drives Inflammation in Atopic Dermatitis. Immunity 42:756-766.
  15. West, C. E., P. Rydén, D. Lundin, L. Engstrand, M. K. Tulic, and S. L. Prescott. 2015. Gut microbiome and innate immune response patterns in IgE-associated eczema. Clinical & Experimental Allergy:n/a-n/a.
  16. van Nimwegen, F. A., J. Penders, E. E. Stobberingh, D. S. Postma, G. H. Koppelman, M. Kerkhof, N. E. Reijmerink, E. Dompeling, P. A. van den Brandt, I. Ferreira, et al. 2011. Mode and place of delivery, gastrointestinal microbiota, and their influence on asthma and atopy. J Allergy Clin Immunol 128:948-55 e1-3.


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