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    Issue Date: July 2024

    Infants’ Microbiomes Have a Circadian Rhythm

    • The study aimed to explore what types of supplements make formula most similar to breast milk.
    • The metabolites produced by the bacteria differ in breastfed versus formula-fed infants, and infants fed formula supplemented with a type of milk sugar called galacto-oligosaccharides have metabolites most similar to those in breastfed infants.
    • Bacteria in infant microbiomes fluctuate in abundance over a 24-hour cycle.
    • The microbes retain a circadian rhythm even when grown outside of the body.

    Bacteria in the guts of infants as young as two weeks old fluctuate in abundance over a 24-hour period, according to a new study [1]. The gut microbiome in adults has a similar circadian rhythm, and growing evidence links its dysregulation to disease [2]. But researchers did not previously know at what point during development it emerges. 

    The study also found that the composition of metabolites in the gut – molecules produced by the gut microbiome — differed strongly between breastfed and formula-fed babies. The functional effects of this difference are not known, but “[w]e can conclude that breast milk does something completely different in the metabolism in the infants’ intestines,” says Dirk Haller, a microbiologist at the Technical University of Munich, in a press release. 

    The study is part of a longstanding effort among researchers to improve how well infant formula can approximate human milk. Special sugars in human milk are known to feed bifidobacteria. The researchers set out to test how well different supplements in formula boosted levels of bifidobacteria in infants’ guts. In a randomized controlled trial consisting of 210 infants, they gave infants formula alone, formula containing bifidobacteria, formula containing milk sugars called galacto-oligosaccarides (GOS), and formula containing both bifidobacteria and GOS. The researchers compared the effects of these different versions of formula to the effects of breast feeding on the gut microbiomes by collecting stool samples from infants at age 2 weeks, 3 months, 7 months, 12 months, and 24 months. They also compared stool samples taken in the daytime to those taken at night.

    The diversity of bacteria increased over time in all the groups, and the composition of the microbial communities varied widely across individuals. Diet only minimally affected   microbiome development compared to age, as the microbiome is highly dynamic during the first two years. Overall, the researchers found that the formula supplemented with GOS did a better job of boosting numbers of bifidobacteria—microbial species  thought to be health-promoting—compared to other formulas studied [3]. 

    The researchers analyzed the composition of metabolites in the different groups at three months – the timepoint at which infants would consume the highest amount of milk or formula but not yet solid foods. Metabolite profiles in the formula-fed groups were significantly different from the breastfed group, they found. “None of the three types of supplementation investigated in this study were able to fully recreate the breastmilk-related microbial environment,” the authors write in the paper. 

    In all groups, however, both metabolite and microbial composition fluctuated rhythmically over a 24-hour cycle. This phenomenon was present in all groups examined but grew stronger over time. The number of rhythmic bacteria increased over time, however, as infants began to eat foods beyond breastmilk or formula. The researchers also grew bacteria from the 3-month stool samples and found that they had a circadian rhythm even in a dish outside the microbiome. 

    Previous work has shown that the circadian rhythm of the gut microbiome in adults both affects and is affected by the circadian rhythm of the human host [4]. The fact that this periodicity is seen in infants “is fairly surprising because it suggests that the bacteria have some intrinsic mechanism that provides some sort of adaptation to a day and night cycle, which could potentially give them an advantage in colonizing the human intestine,” said Haller in the press release.  

    Many questions remain about how exactly the bacteria regulate their circadian behavior, the authors write. They plan to search for the genes regulating these rhythms and to examine whether individual species are able to do so apart from the community as a whole.  


    1. Heppner N, Reitmeier S, Heddes M, Merino MV, Schwartz L, Dietrich A, List M, Gigl M, Meng C, van der Veen DR, Schirmer M, Kleigrewe K, Omer H, Kiessling S, Haller D. Diurnal rhythmicity of infant fecal microbiota and metabolites: A randomized controlled interventional trial with infant formula. Cell Host Microbe. 2024 Apr 10;32(4):573-587.e5.
    2. Reitmeier S, Kiessling S, Clavel T, List M, Almeida EL, Ghosh TS, Neuhaus K, Grallert H, Linseisen J, Skurk T, Brandl B, Breuninger TA, Troll M, Rathmann W, Linkohr B, Hauner H, Laudes M, Franke A, Le Roy CI, Bell JT, Spector T, Baumbach J, O’Toole PW, Peters A, Haller D. Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes. Cell Host Microbe. 2020 Aug 12;28(2):258-272.e6.
    3. Liu J, Tan Y, Cheng H, Zhang D, Feng W, Peng C. Functions of Gut Microbiota Metabolites, Current Status and Future Perspectives. Aging Dis. 2022 Jul 11;13(4):1106-1126.
    4. Heddes M, Altaha B, Niu Y, Reitmeier S, Kleigrewe K, Haller D, Kiessling S. The intestinal clock drives the microbiome to maintain gastrointestinal homeostasis. Nat Commun. 2022 Oct 14;13(1):6068.

    DNA Damage as a Cue to Trigger Milk Production

    • Mammary glands have many cells with several-fold higher DNA levels and more than one nucleus. 
    • Reducing the number of these cells lowers the expression of genes that encode milk proteins such as casein. 
    • Physiological DNA damage might be crucial to successful lactation. 

    When copying their DNA for a daughter cell, human cells act like good math students, pausing to check their work for errors and correcting mistakes as they go. The moments they pause, known as checkpoints, are critical to avoiding harmful mutations or other errors that might cause a descendant to go astray. But when forced to work faster, cells accumulate mutations with no time to pause or fix them. 

    A pileup of errors would usually cause cells to stop multiplying so damaged DNA doesn’t make its way into new cells. Now, a new study suggests that this damaged DNA can trigger processes essential to milk production in mammary gland cells in mice [1]. 

    Typically, a replicating cell begins by making a copy of its DNA. Then, the nucleus divides into two, and finally, the cell itself multiplies to produce two daughter cells. Decades ago, researchers reported that during lactation, mammary glands often contained cells with double the normal amount of DNA, suggesting the cells had copied their DNA but not then divided it amongst daughter cells. “It’s been known for quite a while,” says Lindsay Hinck, a developmental biologist at the University of Santa Cruz, senior author of the new work. However, Hinck adds, the observation “didn’t seem like the end of the story” to Rut Molinuevo, a postdoctoral researcher who was the first author on the study. 

    In her earlier research, Molinuevo had found that when DNA is damaged, a cell can stop the process of replication after DNA division but before cell division, so the cell ends up with two copies of its genome. If cells pause long enough at this point, they start over again from the beginning rather than resuming where they paused. As a result, some cells might end up with multiple copies of DNA.

    In the new study, Hinck, Molinuevo and their co-authors investigated why so many cells in the mammary gland underwent this process. The researchers began by testing the DNA content of mammary cells from pregnant and lactating mice. They found that about 35 percent of cells had double the DNA content within a single nucleus, and several cells with multiple copies of DNA were both single and double- nucleated, suggesting that these cells had halted at different points in the cell cycle. 

    The researchers then tested whether DNA damage played a part in the formation of these cells. When they treated a mouse mammary cell line with a DNA damaging chemical, they found that the cells – rather than dying from the damage – began to carry multiple copies of DNA and started to differentiate into milk-producing cells. Injecting the disruptive chemical into mouse mammary glands also led to an increase in cells with multiple copies of DNA as well as an increase in the expression of genes that make milk proteins. “We think of DNA damage as scary, but in this case it seems to serve a good purpose,” Hinck said. 

    To understand the cellular drivers of these changes, the researchers homed in on a checkpoint inhibitor protein named CDK1, which typically checks DNA for errors and stops the cell cycle if they’re found. They found that blocking CDK1’s activity in cultured mammary cells led to greater expression of genes for milk proteins.  

    The researchers found that in mouse mammary glands, a protein named Wee1, which is known to block CDK1, increased in early pregnancy, again when cells were increasing their DNA content, and again at the start of lactation. They found that treating an organoid model of the mouse mammary gland with a Wee1 inhibitor led to fewer cells with several-fold higher DNA and a decrease in the expression of genes encoding milk proteins. 

    To confirm Wee1’s role, the team then developed a mouse strain where they could block Wee1 production. When they did so, they found that pups didn’t survive past a few days of birth and had no milk in their stomachs, and mothers only produced half as much milk as a control group of mice with normal Wee1 levels. 

    Repurposing DNA damage to serve as a cue to start milk production might have been a useful evolutionary tactic, Hinck said. “You have to build a milk supply in a very limited amount of time,” she explains, and the necessary speed leads to a compromise in the accuracy of DNA replication. But in a deft evolutionary twist, mammary cells might be able to use the accumulation of cells with too much DNA as a cue to start producing milk. When lactation ceases, it’s possible – although yet to be confirmed – that cells with larger amounts of DNA are targeted for clearance while the progenitor cells can remain unharmed, Hinck explained. 

    Although the results need to be validated further, they could eventually lead to non-hormonal ways to increase milk production in dairy animals, Hinck said.


    1. Molinuevo R, Menendez J, Cadle K, Ariqat N, Choy MK, Lagousis C, Thomas G, Strietzel C, Bubolz JW, Hinck L. Physiological DNA damage promotes functional endoreplication of mammary gland alveolar cells during lactation. Nature Communications. 2024 Apr 17;15(1):3288.

    New FDA-Backed Qualified Claim: Yogurt Lowers Diabetes Risk

    • After reviewing limited scientific evidence, the United States Food and Drug Administration (FDA) announced its first qualified health claim for a food: yogurt. 
    • Yogurt manufacturers can now claim that regular consumption of milk-based yogurt can reduce the risk of type 2 diabetes.  
    • Nutrition experts note that yogurt alone cannot cure or prevent type 2 diabetes. It is meant to supplement a healthy diet and lifestyle.

    For thousands of years, yogurt has been recognized as a healthy staple in the human diet [1]. Studies have shown that yogurt can improve mental health, reduce inflammation, boost gut health, and lower the risks of cardiovascular disease and type 2 diabetes.

    Yet, it wasn’t until a few months ago that the United States Food and Drug Administration (FDA) acknowledged the growing body of scientific evidence regarding the health benefits of yogurt [2]. 

    In its first-ever qualified health claim for a food, the FDA announced that yogurt manufacturers can now claim, “Eating yogurt regularly, at least 2 cups (3 servings) per week, may reduce the risk of type 2 diabetes according to limited scientific evidence” [2]. The announcement was made in response to a petition submitted by Danone North America in 2019. 

    Qualified health claims, like this one, are supported by scientific evidence but do not meet the more rigorous standards required for an “authorized health claim” [3]. Danone’s petition cited 117 publications on the relationship between yogurt and type 2 diabetes [2]. The FDA primarily focused on the observational studies containing human data and found that, of these, 28 of the publications had sufficient data to draw conclusions about the link between the two [2, 4].

    Ronan Lordan, a postdoctoral researcher at the Institutional for Translational Medicine and Therapeutics at the University of Pennsylvania, says in a new article published in Diabetes & Metabolic Syndrome: Clinical Research & Reviews that this is the first time the FDA has approved a qualified health claim about a single food, rather than an ingredient or other component, which has traditionally been the case [4].

    “It is notable that the FDA did not single out any one nutrient as the responsible agent for the potential health benefits described,” says Lordan. “This is likely because many constituents, including lipids, proteins, and minerals, within yogurt have been associated with various cardiometabolic health effects.” 

    Critics to the health claim noted that yogurt can be high in added sugar [2, 5], and by approving it, the FDA may inadvertently increase the prevalence of type 2 diabetes [2]. This is particularly concerning in the United States, where 97.6 million adults are already prediabetic.   

    “It is a valid concern,” Lordan says. “However, the FDA concluded that the benefits of yogurt consumption appeared to be independent of the sugar or fat content.” In other words, the association between yogurt and the reduced risk of type 2 diabetes was statistically significant regardless of how much sugar or fat was in the yogurt. 

    The FDA was more concerned that the high added sugar content of some yogurts may contribute empty calories, adding little to no nutritional value to a person’s diet. The agency noted that yogurt manufacturers should consider this before adding the health claim to their products [2]. 

    Regardless, Lordan adds that if reducing the risk of type 2 diabetes is a primary health goal, consumers should try to reach for a milk-based yogurt with minimal added sugars. 

    “Consumers and healthcare providers should be aware that yogurt consumption alone will not prevent type 2 diabetes,” Lordan says. “It must be consumed as part of a healthy diet and lifestyle. One food alone cannot prevent type 2 diabetes.” 


    1. Fisberg M, Machado R. History of yogurt and current patterns of consumption. Nutrition Reviews. 2015;73(suppl_1):4-7.
    2. U.S. Food & Drug Administration. Petition for a qualified health claim for yogurt and reduced risk of type 2 diabetes mellitus (docket no. FDA-2019-p-1594) U.S. Food & Drug Administration; 2024 [Available from:
    3. U.S. Food & Drug Administration. Qualified health claims: U.S. Food & Drug Administration; 2024 [updated March 28, 2024. Available from:
    4. Lordan R. A new era for food in health? The FDA announces a qualified health claim for yogurt intake and type II diabetes mellitus risk reduction. Diabetes Metab Syndr. 2024;18(4):103006.
    5. Moore JB, Horti A, Fielding BA. Evaluation of the nutrient content of yogurts: A comprehensive survey of yogurt products in the major uk supermarkets. BMJ Open. 2018;8(8):e021387.

    Hot Topic: Heat Treatment Influences Milk Protein Digestion

    • Standard treatments that increase cow milk’s microbial safety can influence the structure of milk proteins but do not reduce the protein content of milk.
    • Female adults in a randomized, controlled trial digested ultra-high temperature milk more slowly than pasteurized milk, however ultra-high temperature milk was associated with a more rapid release of amino acids into the bloodstream.  
    • For most consumers, these digestive differences may not be significant, but there are some populations where a rapid release of amino acids would be beneficial.

    When it comes to pasteurization, cow milk proteins can take the heat—to a certain degree. Although boiling cow’s milk can reduce protein levels, neither high-temperature short-time (HTST) pasteurization nor ultra-high temperature (UHT) processing decreases the protein content of cow’s milk. 

    “Heat treatment doesn’t destroy milk protein,” explains Dr. David Dallas, Associate Professor in the Nutrition Program of the College of Health at Oregon State University. “It isn’t that proteins are nutritionally damaged, it is more about their bioactivity and structure.” 

    For human consumers, these structural changes could influence the way milk proteins are digested, including how they are broken down, absorbed, and utilized by the body [1-3]. 

    Heat treating milk isn’t new—pasteurization techniques have been used for over a century to increase milk’s microbial safety and shelf life. It seems surprising, then, that there have only been a handful of studies addressing how different milk heat treatment methods affect nutrient delivery of protein in humans [3, 4]. 

    “Heating intensity is very interesting for bovine milk proteins,” explains Dr. Kasper Hettinga, Professor of Food Sciences and Agrotechnology at Wageningen University. Whey proteins, which make up 20% of milk protein, are heat sensitive and denature when heated. Although denaturing sounds like a negative, Hettinga shares that “it can actually make the proteins easier to digest.” 

    Milk’s whey proteins have a three-dimensional structure—imagine a ball of yarn that has been quickly wound up and has twists, turns, and tangles. To digest whey protein requires unwinding and untangling this three-dimensional structure into one long string of amino acids, then snipping apart the peptide bonds that link the amino acids. Denatured whey proteins arrive in the digestive tract already a bit untangled, allowing the digestive enzymes to release the individual amino acids in a shorter amount of time [2].

    Casein proteins, which make up the other 80% of cow milk protein, respond differently to heating than most food proteins [2]. “Caseins are more flexible molecules and do not lose their structure when heated,” says Hettinga. Instead of a tangled ball of yarn, casein proteins are more spherical in shape. These small spheres, called casein micelles, are usually digested more slowly than whey proteins because they form a curd in the digestive tract when enzymes start to break them apart. However, in vitro models of digestion suggest that increasing the temperature of milk, as is done with UHT processing, can result in a more crumbled or fragmented curd, which would promote more rapid casein digestion [2].  

    A new study [1] from a team of researchers in New Zealand provides one of the most comprehensive and systematic studies on the digestive kinetics of heat-treated milk proteins to date. Combining MRI technology and blood biochemistry, the researchers compared digestive rates and nutrient delivery of cow milk proteins from two standard heat treatments. Based on results from in vitro digestion simulations and animal models, they predicted that the higher temperature used by UHT treatments (preheated 95° C, 90 seconds, processed 140° C, 4 seconds) compared with HTST pasteurized milk (75° C, 15 seconds) would result in faster gastric emptying and thus a faster delivery of nutrients to the bloodstream.

    In the study, each of the 20 female adult participants consumed both HTST pasteurized milk (PAST-M) and UHT treated milk (UHT-M). Participants were randomly assigned which milk they would consume first, and both participants and researchers were blinded as to the type of milk participants were drinking. There were three to 28 days of “washout” between consumption of each milk type to minimize any cross-over effects of study procedures. Participants consumed identical dinners and then fasted starting from 10pm on the night prior to consuming each intervention milk sample. On the morning of the intervention, participants drank 500ml of refrigerated milk and then had MRI scans of their gastric contents after 5, 10, 20, 30, 60, 90, 120, and 180 minutes and venous blood draws after 20, 30, 40, 60, 90, 120, 240, and 300 minutes. 

    As predicted, amino acids showed up more quickly in blood samples after UHT-M consumption compared with PAST-M. However, this faster release of amino acids was not because of faster milk digestion; contrary to results from in vitro models, gastric contents emptied more slowly after consuming UHT-M, particularly during early digestion [1]. MRI scans suggest that casein proteins from UHT milk formed a clot with less dry matter (and more water), which stayed in the stomach longer than the dense clot formed by PAST-M caseins [1]. The study authors suggest that the rapid release of nutrients associated with UHT-M, including branched chain amino acids and essential amino acids, were part of the liquid (whey) phase that was not restricted within the casein curd [1].  

    HTST pasteurized milk, which is the most consumed milk in the U.S. [4], was associated with a slower release of amino acids but faster gastric emptying, whereas UHT milk, which is more shelf stable, had a faster release of amino acids but slower gastric emptying—but is one digestive pattern more optimal than the other? 

    “Milk is the gold standard when it comes to protein nutrition and digestibility,” explains Dallas. “Compared with soy protein which has low bioavailability and low digestibility, 100 percent of the milk protein you consume will be digested by humans, with or without heat treatments.” 

    However, there may be clinical applications where a faster delivery of amino acids could be advantageous [1]. “For the average human adult drinking either [pasteurized or UHT] milk, it isn’t that one milk type is going to be much better,” says Hettinga. “But there may be benefits for specific target groups, like the elderly.” Hettinga explains that as humans age, their digestion slows down. A more rapid release of branched chain amino acids, particularly leucine, that help stimulate protein synthesis in skeletal muscle could be especially beneficial for this population. 

    Cow milk is an important source of high quality protein for humans of all ages [2]. The results from this study suggest that commonly used heat treatments can be an effective way to control physiological responses and enhance the delivery of essential nutrients [1]. 


    1. Milan AM, Barnett MP, McNabb WC, Roy NC, Coutinho S, Hoad CL, Marciani L, Nivins S, Sharif H, Calder S, Du P. The impact of heat treatment of bovine milk on gastric emptying and nutrient appearance in peripheral circulation in healthy females: a randomized controlled trial comparing pasteurized and ultra-high temperature milk. The American Journal of Clinical Nutrition. 2024 May 1; 119(5): 1200-15.
    2. van Lieshout GA, Lambers TT, Bragt MC, Hettinga KA. How processing may affect milk protein digestion and overall physiological outcomes: A systematic review. Critical Reviews in Food Science and Nutrition. 2020 Aug 5;c60(14): 2422-45.
    3. Fatih M, Barnett MP, Gillies NA, Milan AM. Heat treatment of milk: a rapid review of the impacts on postprandial protein and lipid kinetics in human adults. Frontiers in Nutrition. 2021 Apr 30; 8: 643350.
    4. Lacroix M, Bon C, Bos C, Léonil J, Benamouzig R, Luengo C, Fauquant J, Tomé D, Gaudichon C. Ultra high temperature treatment, but not pasteurization, affects the postprandial kinetics of milk proteins in humans. The Journal of Nutrition. 2008 Dec 1; 138(12): 2342-7.

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