Showing posts with label microbiome. Show all posts

Tuesday, December 20, 2022

Mice With a Healthy Gut Microbiome Are More Motivated to Exercise

reposted from https://www.the-scientist.com/news-opinion/mice-with-a-healthy-gut-microbiome-are-more-motivated-to-exercise-70845?utm_campaign=TS_DAILY_NEWSLETTER_2022&utm_medium=email&_hsmi=238698979&_hsenc=p2ANqtz-_ymMGFDXk8FwZj9ol6Ge0rVxC-_oiDn4m4ofgcFD6cZlpoxtOelPBFQEdpq6BDv4MMh_wFge2mwPYQOnZ3Dz61bMwgUQ&utm_content=238698979&utm_source=hs_email Mice With a Healthy Gut Microbiome Are More Motivated to Exercise A neural pathway between the gut and the brain led to the release of dopamine when the mice ran on a wheel or treadmill, but only in the presence of a robust microbiome. a white mouse sits on a blue exercise wheel, looking out onto the shavings below A black and white headshot of Katherine Irving Katherine Irving Dec 16, 2022 | 4 min read PDF VERSION ABOVE: © ISTOCK.COM, MARY SWIFT The gut is a jungle teeming with microorganisms that are instrumental to the process of digesting food, regulating metabolism, and defending against infection. However, research now suggests yet another way that the gut microbiome’s influence extends far past the bounds of its abdominal home. In mice, gut bacteria stimulate the production of dopamine during exercise, without which the mice lack the motivation to continue running, scientists at the University of Pennsylvania reported December 14 in Nature. “This is the most comprehensive study I have ever seen,” says Theodore Garland Jr., an evolutionary physiologist studying the gut-brain axis in mice at the University of California, Riverside, who wasn’t involved in the research. “[It’s] pulling together lots of different pieces that we knew before in different contexts or in isolation of other parts in a way that hasn’t been done before.” Exercise is “the single most effective lifestyle intervention that we have that protects us from a very large range of diseases,” says study coauthor Christoph Thaiss, a microbiologist at the University of Pennsylvania Perelman School of Medicine. Yet despite being a very physical activity, he says the success of an individual’s attempts to exercise often depends on their mental state. “If you look at what elite athletes say, many of them will say that they are not necessarily physically better than their competitors, but their mind is very well prepared,” he says. “But when it comes to preparing athletes, mentally or motivationally, for their competitions, there’s very little scientific evidence of how these methods might work.” Previous research had already found that the gut microbiome can influence muscle tissue and cardiovascular fitness as well as brain chemistry. But Thaiss aimed to bring such findings together and examine the broader role of the gut microbiome in exercise performance. So, he and his colleagues set up an experiment using 199 outcrossed mice from eight different genetic backgrounds to ensure that any findings weren’t limited to one strain. Using multiple antibiotics, the researchers altered the mice’s microbiome communities: some mice had fully functioning microbiomes, while the others had their gut microbiomes either partially or entirely removed. See “Tinkering with Gut Microbes Boosts Brain Plasticity in Mice” They then tested each mouse’s performance while running in two different settings: a treadmill, on which the mice were forced to run for an extended period to test their endurance, and a wheel, on which the mice were allowed to run as often and for as long as they wanted. Although all the mice were equally capable of moving around their cages, the mice with reduced microbiomes tired more quickly when exercising on the treadmill than mice with robust microbiomes. They also spent less time on the wheel, which the researchers attributed to reduced motivation to exercise. Thaiss then searched for a neural explanation for the behavioral differences among the groups of mice. He and his team used RNA sequencing to analyze the mice’s striatal spiny neurons, which are involved in producing the behavior-reinforcing neurotransmitter dopamine both before and after exercise, and found that many of the genes normally expressed during exercise were dampened without the microbiome. When he performed an experiment limiting dopamine production during exercise by inhibiting these neurons, it had the same effect that limiting or entirely removing the microbiome had in the previous experiment. From these experiments, Thaiss inferred that the production of dopamine was a significant factor in a mouse’s propensity to exercise, and that a mouse’s gut microbiome composition played some role in the regulation of dopamine in its brain. That led him to conclude that the mice lacking gut bacteria didn’t experience the dopamine rush animals usually get through exercise, known as the “runner’s high.” “If we can remote[ly] control the brain from the perspective of the GI tract, then this becomes a much more accessible problem.” —Christoph Thaiss, University of Pennsylvania Perelman School of Medicine The question then became how microbes in the gut influence dopamine in the brain. To find out, the team inhibited a set of neurons that connects the gastrointestinal tract to the brain using formulated drugs. In the same wheel and treadmill experiments as before, mice with healthy microbiomes but inhibited gut-brain neurons exhibited reduced exercise rates on par with the mice with limited microbiomes, suggesting that it was the stimulation of these neurons that controlled the amount the mice exercised. Finally, the researchers treated mice with specific antibiotics to determine what kinds of microbes were triggering the neurons. They performed a metabolomics analysis to determine which bacterial metabolites triggered the neural response. They found that metabolites known as fatty acid amides (FAAs) made by some microbes found in a healthy mouse gut were the most active during exercise. These FAAs generate neurotransmitters known as endocannabinoids. The scientists performed more experiments using ingestible inhibitors to determine that the endocannabinoids produced by the bacteria’s FAAs were stimulating receptors in the GI tract neurons during exercise, thereby triggering the neurons that subsequently stimulated dopamine production in the brain. “It was really elegant the way they structured the entire story,” says Francesca Ronchi, an immunologist at the Institute of Microbiology, Infectious Diseases and Immunology in Berlin, Germany who wasn’t involved in the study. She adds that she was very impressed by the thoroughness of the paper. “You couldn’t do it better.” Thaiss says that the next step will be to take this research from mice to humans and determine whether the same pathway exists in us. Garland explains that analyzing motivation in humans is more complicated than it is in mice: a person’s incentive to exercise is based on many more factors, including external ones such as their social environment and influence from family or friends, than is a mouse’s. “We don’t go and give our mice pep talks when they run a lot on the wheel,” he observes. In humans, by contrast, those that are naturally talented at some form of exercise may receive more praise, fueling them to exercise more. See “Regular Exercise Helps Patients Combat Cancer” Nonetheless, Ronchi says findings like these could one day reveal ways to stimulate exercise in those who need it, including cancer, Parkinson’s, or Alzheimer’s patients, for whom exercise is a valuable tool in mitigating symptoms. After all, if such a pathway does exist in people, gut microbes may be easier to manipulate or influence than neurons in the brain, Thaiss suggests: Unlike neurons, which are finicky and often inaccessible, gut bacteria could be influenced by an ingestible treatment. “If we can remote[ly] control the brain from the perspective of the GI tract, then this becomes a much more accessible problem,” he says. “But that’s still science fiction for now.” Keywords: bacteriaexercisefitnessgut bacteriagut microbiotaimmunologymicrobiologymicrobiomemicrobiotamouse studyneural activationneuronneurotransmittersNewspathwaysignaling pathwaysstudy story

Friday, June 24, 2022

Study Links Depression with High Levels of an Amino Acid

reposted from

Study Links Depression with High Levels of an Amino Acid

Experiments in animals and observations in humans suggest that the amount of proline circulating in one’s plasma has a strong association with depression severity.

Dan Robitzski

Jun 14, 2022

ABOVE:Bacteria in the gut© ISTOCK.COM, ARTUR PLAWGO

A growing body of literature ties the gut microbiome to symptoms of depression in a seemingly circular relationship where each affects the other. However, many of the studies on this relationship merely link certain bacterial populations or diets to major depressive disorder—leaving open critical questions about the underlying mechanisms of how the gut microbes might influence depression.

Research published last month (May 3) in Cell Metabolism takes an important step toward filling such gaps, demonstrating in multiple animal species that there is likely a causative relationship between depression severity and serum levels of the nonessential amino acid proline, which the study finds depend on both diet and the activity of proline-metabolizing bacteria in the gut.

“To the best of my knowledge, this is the first time that a team actually demonstrates a causal relationship between proline intake and depressive behavior,” King’s College London metabolism researcher Sandrine Claus, who didn’t work on the study and is also chief scientific officer of the microbiome therapeutics company YSOPIA Bioscience, tells The Scientist over email. “I am unaware of a proline-mediated gut-brain axis. This is therefore a completely novel mechanism of action.”

Depression diet: the effects of proline

Previous research had found that proline, among other dietary compounds, seems to play a role in major depressive disorder, but “we found increased levels not only [in] major depression but also in subjects with moderate depression,” study coauthor José Manuel Fernández-Real, a researcher at the Girona Biomedical Research Institute and Dr. Josep Trueta Hospital, both located in Spain, explains. Indeed, the severity of the symptoms correlated with the subjects’ circulating proline.

Fernández-Real and his colleagues uncovered this when they compared people’s responses on an 80-item food intake questionnaire with scores on the Patient Health Questionnaire-9 (PHQ-9), a common clinical survey for diagnosing and measuring the severity of a person’s depression. Out of all the dietary nutrients in the questionnaire, Fernández-Real says, the one “most associated with depressive traits was precisely proline.” Blood tests in the same participants solidified the correlation between proline and depressive traits.

See “Gut Microbes May Play a Role in Mental Health Disorders”

However, some discrepancies emerged within the data that demanded a closer look. “Not all subjects with increased proline in the diet had increased proline in the plasma,” hinting that some yet-undiscovered factor was involved, Fernández-Real explains. In search of that explanation, he and the other researchers determined the microbiome compositions of the human participants.

The paper notes that most previous studies attempting to do the same failed to achieve bacterial species-level resolution and have reached inconclusive and conflicting findings. But Fernández-Real and colleagues employed a multi-omics approach that allowed them to link microbial function to the specific biological pathways associated with depression, granting their study a level of resolution that Fernández-Real says was lacking from what he describes as underpowered previous studies.

In the study participants, plasma proline levels were associated with the presence and activity of specific gut bacteria—people with high proline consumption and higher plasma proline levels had different microbiome compositions than those who consumed the same amount of proline but had less circulating in their blood. Furthermore, the team found that the microbial communities of the former were associated with more severe depression.

How the gut microbiome influences depression

To determine whether there’s a direct link between proline and depression, the researchers revisited and modified mouse and Drosophila melanogaster models that they’d previously used to study how the microbiome influenced cognitive abilities.

See “Bacterial Metabolite May Regulate Cognition in Mice”

The researchers fed 10 mice a standard diet and another 10 a proline-supplemented diet, then subjected them to stressors typically used to trigger depression-like behaviors. After six weeks, the experimental group had significantly higher proline levels circulating in their plasma and exhibited more signs of depressive behaviors, such as a disinterest in sugar water and decreased mobility during a tail suspension test.

To see how the microbiome factored in, the researchers took fecal samples from 20 human volunteers (nine of whom had high proline levels and all of whom demonstrated a direct correlation between their PHQ-9 score and circulating plasma proline) and put them into antibiotic-treated mice, effectively transferring the human microbiomes into the animals. When the mice were subjected to another test meant to induce depressive behaviors, the researchers found that the mice’s behavior correlated with the PHQ-9 scores—and therefore circulating proline levels—of their donors as well as the mix of microbes now residing in their guts.

The data demonstrated that “a particular microbiota metabolizes proline and is critical to develop more or less depressive symptoms,” says Fernández-Real.

See “Human Gut Microbe Transplant Alters Mouse Behavior”

The researchers also conducted RNA sequencing of the animals’ prefrontal cortex, a region of the brain associated with cognition. That revealed that genes related to depressive behaviors had been upregulated following fecal transplantation—and that expression of the proline transporter gene Slc6a20 in the brain correlated with the mice’s behavior and their microbe donors’ PHQ-9 scores.

“The microbiota from subjects with the highest depression scores induced emotional traits in the mice,” says Fernández-Real. “Interestingly, the prefrontal cortex of transplanted mice showed increased expression of genes . . . that we also found in the intestine of subjects with increased proline intake.”

From there, the researchers moved on to Drosophila experiments, subjecting both wild type control flies and those with downregulated CG43066—the Drosophila version of sl6a20—to stressors to see if the transporters affect whether the animals exhibit depressive behaviors. They then ran the same tests on Drosophila colonized with the bacteria found to increase or decrease proline metabolism in the prior experiments. Downregulating the proline transporter gene or colonizing the Drosophila with specific bacteria, especially certain Lactobacillus species, seemed to protect the flies from depressive behavior, the study found.

Animal depression, human questions

The researchers weren’t able to conduct similar experiments in people, which they concede limits the conclusions that can be drawn from their work. Going forward, Fernández-Real says it will be important to test, for example, “whether diets with different proline contents influence depressive traits and depressive symptomology.”

Chrysi Sergaki, a microbiome researcher at the Medicines & Healthcare products Regulatory Agency in the UK who did not work on the study, tells The Scientist over email that “using these [animal] models is a start. They can help us understand the impact of the microbiome on brain function, but that doesn’t necessarily mean that it will work the same way in humans.” Still, she says that because similar experiments can’t be performed on humans, the animal models used in the new study can grant researchers “a deeper understanding of how the microbiome can influence the functions of the organism they live in,” adding that “that knowledge can be valuable in the way we think about the microbiome when we move to humans.”

See “Distinct Microbiome and Metabolites Linked with Depression”

Claus expresses similar sentiments. “Modeling depressive behaviors in animals is . . . very challenging,” she writes. “I actually thought that the drosophila model was interesting despite the fact that we cannot directly translate behavioral observations from drosophila to humans. These are useful to study mechanisms of action though.”

Still, Claus adds that a lack of data on circulating proline levels in the mouse model, combined with repeated reanalysis of the same cohort of people, make it difficult to draw definitive conclusions about the mechanism of microbial proline metabolism and its link to depression.

“The authors keep reanalyzing the same cohort, insisting that they always find a consistent microbial signature with PHQ-9 and proline,” Claus writes. “But this is not surprising since proline is correlated to PHQ-9 score in this cohort, and PHQ-9 score is correlated with a microbial signature.”

Sergaki applauds the study authors for describing the limitations of their work, adding that microbiome studies are notoriously difficult to reproduce and therefore validate. “I think all microbiome scientists look at these studies with a critical eye,” she tells The Scientist. “The authors mention certain limitations of their study which are quite important. The biggest question is always this: correlation or causation? Due to the complexity of the system, this is very difficult to answer.”

Friday, December 25, 2020

The Infant Gut Microbiome and Probiotics that Work

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https://www.the-scientist.com/features/the-infant-gut-microbiome-and-probiotics-that-work-67563?utm_campaign=TS_DAILY%20NEWSLETTER_2020&utm_medium=email&_hsmi=104126996&_hsenc=p2ANqtz-8cSk5-k-om1lDRx7LxTdmgai1oXXIz4s2_qJk7bIl5JENdubpGDyj2FnGlkRm4qoWc-ryG--pV0JPABSGF3ZM0ie7ARw&utm_content=104126996&utm_source=hs_email

The Infant Gut Microbiome and Probiotics that Work

The gut microbiome is more malleable in the first two years after birth, allowing probiotics to make their mark. Can we exploit this to improve infants’ health?

Jennifer T. Smilowitz and Diana Hazard Taft

Jun 1, 2020

ABOVE: MODIFIED FROM © ISTOCK.COM, HOMUNKULUS28; © ISTOCK.COM, TATIANA VASILYEVA

In the fall of 2018, a team of researchers from the Weizmann Institute of Science in Israel published findings that a cocktail of 11 strains of Lactobacillus and Bifidobacterium had minimal immediate impact and no lasting effect on the makeup of the gut microbiome of mice or people. In fact, the probiotic bacteria were not found in any of the fourteen adult participants after supplementation ended.

These recent findings received quite a lot of press and added to growing sentiment among the public that probiotics—live microorganisms that are purported to confer benefits on the human host—don’t work. Decades of research have shown that most probiotics aren't able to colonize or exert lasting benefits in the human gut. Some critics even suggested that probiotics may not be a promising avenue for treating disease or otherwise improving health and wellness. But we thought: “Don’t throw the baby out with the bathwater—our work shows that the right probiotic can work in the infant gut.” Findings we published in 2017 showed that feeding breastfed babies a probiotic that included a specific strain of Bifidobacterium longum subspecies infantis (B. infantis EVC001) resulted in a 10,000,000-fold average increase in levels of fecal B. infantis. This level persisted for one month after the supplement was consumed, and levels remained elevated for up to one year after treatment.

To understand why the infant gut microbiome changed so drastically over the past century, we sought to understand how the infant gut microbiome forms.

Colonization of the infant gut by B. infantis had protective effects, such as lower levels of potential gut pathogens and fecal endotoxin, an outer membrane component of Gram-negative organisms known to trigger inflammation. We also found that infants given the B. infantis probiotic had reduced intestinal inflammation compared with breastfed infants who did not receive the probiotic. The gut microbiomes of B. infantis supplemented babies harbored fewer antibiotic resistance genes—a sign of fewer pathogens—and showed less degradation of mucin, a glycoprotein secreted by the intestinal epithelium that protects epithelial cells from direct contact with gut microbes. These data support earlier findings from Mark Underwood and colleagues at the University of California, Davis. In 2013, Underwood’s team showed that feeding preterm infants a different strain, B. infantis ATCC15697, resulted in greater increases in fecal Bifidobacterium and reduced levels of potential pathogens compared with infants given a probiotic containing B. lactis.

While the scientific community and the public grappled with repeated findings that probiotic supplements taken by adults are not consistent in effectively colonizing the gut or conferring benefit, we now had convincing evidence that babies’ gut microbiomes responded incredibly well to specific strains of B. infantis. The question was why.

Microbiome origins

Hints about the infant microbiome can be found in century-old articles on commensal bacteria in infant feces. W. R. Logan, a clinical pathologist at the Research Laboratory of the Royal College of Physicians in Edinburgh, was the first to report, 100 years ago, that bacteria in fecal smears from breastfed infants were a near monoculture of Bacillus bifidus, which is today known as the genus Bifidobacterium. Fecal smears from formula-fed infants of that time, by contrast, had a diversity of bacteria, with relatively few Bifidobacterium—more similar to the microbial diversity found in today’s breastfed infants.

These striking changes in the gut microbiome composition seen over the past century were consistent with our recent finding that the fecal pH in breastfed infants dramatically increased from pH 5.0 to 6.5 within the past 100 years, a change associated with an apparent generational loss of Bifidobacterium and concomitant increase in potential pathogens. The reduction in Bifidobacterium in the gut microbiome of breastfed infants is likely an unintended consequence of medical practices that can save lives but do not support the growth of Bifidobacterium. Such medical practices include treatment with antibiotics to which Bifidobacterium are sensitive; infant formula that doesn’t provide the specific food the bacterium requires; and greater numbers of cesarean section deliveries, which bypass the route by which the bacterium is transferred from mother to baby. These medical practices have been implicated in the increased risk for allergic and autoimmune diseases prevalent in resource-rich nations. The reduction in Bifidobacterium and increase in proinflammatory microbes in early infancy is proposed to occur during the critical window of immune system development, and thereby may increase the risk for immune disease later in life.

To understand why the infant gut microbiome changed so drastically over the past century, we sought to understand how this community forms. Infant gut microbiome colonization begins at delivery with exposure to maternal microbes—mostly vaginal and fecal microbes for vaginally delivered babies or predominately microbes from the skin, mouth, and surrounding environment in infants born by cesarean delivery. After birth, infants are bombarded by a vast array of microbes found in the environment, including in breast milk, but the species that go on to become durable members of the microbial community are often those transmitted by the infants’ mothers through physical contact.

Children continue to acquire gut microbiome species from their mothers and others in the community during early life. This stands in contrast to an adult’s gut microbiome, which is stable and resists change largely because the available space and food is already used by established microbes—the ecological niches are simply occupied in adult guts. Thus, it makes sense that a probiotic has a better chance of persisting in the infant gut, where it faces less competition, and therefore is more likely to have food it can consume and a location where it can grow. A probiotic serves as just one more source of exposure to new bacteria for the infant.

Recognizing this, we began to wonder: In our studies, what ecological niche did B. infantis fill that supported its persistence in infants long after probiotic administration stopped?

The Changing Infant Microbiome

Historically, the breastfed infant gut microbiome was a near monoculture of Bifidobacterium (J Pathol Bacteriol, 18:527–51, 1913). The formula-fed infant gut microbiome was much more diverse. The breastfed infant gut microbiome and the formula-fed infant gut microbiome are now more similar to the historical formula-fed infant gut microbiome, although modern breastfed infants do have more Bifidobacterium than modern formula-fed infants.

See full infographic: WEB | PDF

Setting the stage

A major factor in determining which bacteria thrive in the gut is the availability of their carbohydrate food sources. Thus, for a probiotic to work in an infant, microorganisms should be selected so that the food source they use most efficiently matches what’s available—a food that is present and not already being consumed by other bacteria. We set out to determine what carbohydrates B. infantis consumes in the infant gut.

Naturally, we turned to breast milk, which for millions of years has been the single food that can exclusively nourish and protect babies for the first six months of life. Human milk delivers nutrients as well as non-nutritive, bioactive molecules, including carbohydrates known as human milk oligosaccharides (HMOs). Back in the mid-1900s, Paul György, a world-renowned biochemist, nutritionist, and pediatrician from the Hospital of the University of Pennsylvania, and colleagues unknowingly referred to HMOs when they proposed the existence of a “bifidus factor,” something unique in breast milk that fed Bifidobacterium. While humans cannot digest HMOs, it turns out that Bifidobacterium, especially B. infantis, can. In 2007, our group at UC Davis used mass spectrometry–based tools coupled with microbiology to show that B. infantis gobbles up HMOs as its sole energy source, while other species of Bifidobacterium consume only some HMOs in addition to plant-, animal-, and host-derived carbohydrates.

HMOs are a diverse class of complex carbohydrate molecules synthesized by the mammary gland. With approximately 200 different molecular species, they represent the third most abundant solid component in human milk following lactose and fat. Because HMOs are complex and vary in structure, they are expensive to manufacture. Current infant formulas may contain one or two simple HMO structures, but at a fraction of the concentration found in breast milk. Infant formulas lack the abundance and complexity of HMOs to selectively feed beneficial gut microbes and to bind and neutralize pathogens from the gut.

The bacterial species in the infant gut capable of consuming HMOs can be considered the milk-oriented microbiome (MOM). Although B. infantis appears to be the most efficient consumer of HMOs, other species of Bifidobacterium, in particular, B. breve and B. bifidum, can and do consume some HMOs but also consume plant-, animal-, and host-derived carbohydrates. The Bifidobacterium species that colonize the gut change throughout life in response to available carbohydrates in the host diet. For instance, B. infantis, B. breve, and B. bifidum are MOM bifidobacteria typically found in the stool of exclusively breastfed infants, while B. longum and B. adolescentis, which preferentially consume plant- and animal-derived carbohydrates, are typically found in the stool of adults. Yet there is variation and overlap in the species present at different life stages.

A major factor in determining which bacteria thrive in the gut is the availability of its carbohydrate food source.

Of the MOM bifidobacteria found in the infant gut microbiome, different species may have different implications for the microbiome. For example, when we gave exclusively breastfed infants a supplement with the probiotic B. infantis EVC001, their gut became dominated by the genus Bifidobacterium—upwards of 80 percent relative abundance of the gut microbiome—and potential pathogens made up less than 10 percent of the community. On the other hand, the gut microbiomes of exclusively breastfed infants who were not supplemented with B. infantis EVC001 had much lower levels of Bifidobacterium, with only about 30 percent relative abundance, and potential pathogens constituted about 40 percent of the microbes in their gut, findings that are consistent with previous work from our group and others. This near-monoculture of Bifidobacterium appeared to be driven by B. infantis, which represented about 90 percent of the total Bifidobacterium in infants fed the probiotic. In contrast, B. longum was the predominant gut Bifidobacterium in the control group, followed by B. breve and B. bifidum. These data highlight the vital importance of strain specificity in probiotics, and the combination of the presence of B. infantis and breastfeeding to support a protective gut environment in infants.

To understand how supplementary B. infantis can so successfully outcompete other microbes in the infant gut, we took a deep dive into its feeding strategy. Turns out it is a picky eater, exclusively dining on HMOs, and when HMOs are abundant, B. infantis gobbles them up ravenously. Unlike other MOM bifidobacteria, B. infantis possesses all the genes necessary for the complete, internal degradation of HMOs and preferentially uses HMOs over any other carbohydrate source. Other MOM bifidobacteria such as B. bifidum and B. breve strains display growth capabilities with only a subset of HMOs. B. infantis thus has a competitive advantage when breast milk makes up the entire diet.

A 2008 study from colleagues at UC Davis and their collaborators showed how B. infantis makes quick use of HMOs: with binding proteins to grab HMOs from the gut lumen and transporters to usher them into the cytoplasm, breaking them down into monosaccharides that are then fermented into lactate and the short-chain fatty acid acetate that are secreted from the cell. These end products maintain a lower pH in the intestinal milieu, supporting the transport of these compounds into the intestinal epithelium for use by the host and creating an undesirable environment for potential pathogens. The production of acetate also blocks the infiltration of toxic molecules produced by pathogenic bacteria by enhancing intestinal barrier function and inhibiting pro-inflammatory and apoptotic responses. Recent findings from one in vitro study have shown that the amount of acetate and lactate produced by different bifidobacterial species is dependent on how well they consume the carbohydrates available to them. Hence, feed a carbohydrate-consuming microbe its preferred carbohydrate, and it has greater potential to produce more of its protective end-products.

Another reason why B. infantis outcompetes other bifidobacterial strains in the gut of breastfed infants is that all of its HMO digestion happens inside the bacterial cell. B. bifidum, on the other hand, digests HMOs externally. This extracellular digestion liberates simple carbohydrates and may cross-feed other species of Bifidobacterium, but also cross-feeds and thus opens an ecological niche for other, perhaps less beneficial microbes. Cross-feeding among microbes diversifies the gut microbiome, which is considered to be generally beneficial in adults.

But is there an advantage to having a near monoculture of Bifidobacterium in infants? By asking this question, our focus turned to immune development.

The Milk-Oriented Microbiome

Human milk oligosaccharides (HMOs) are complex carbohydrates that microbial species of the milk-oriented microbiome (MOM) can use as a food source. Bifidobacterium infantis encodes many proteins that specifically bind and transport all types of HMOs into its cell and digest them internally. Other Bifidobacterium species digest only some HMOs and some do so externally. Digestion of HMOs by MOM Bifidobacterium results in the production of lactate and the short chain fatty acid acetate, that are secreted into the gut lumen. These molecules lower the pH in the intestinal milieu, which improves their transport into the epithelium for use by the host and creates an undesirable environment for potential pathogens such as E. coli.

B. infantis preferentially consumes all HMO species over any other carbohydrate source.

Binding proteins glom on to HMOs and usher the carbohydrates to transporters that move them into the bacterial cell.
Intracellular glycosyl hydrolases cleave each glycosidic linkage
of all HMO structures, yielding monosaccharides.
These monosaccharides are metabolized into acetate and lactate that are secreted from the cell.

B. bifidum eats only a subset of HMOs.

Glycosyl hydrolases attached to the outer cell membrane break down
HMOs into mono- and disaccharides in the extracellular space.
These molecules are imported via transporters, and some are gobbled up by other intestinal microbes, a process called cross-feeding.
The mono- and disaccharides are further metabolized into acetate and lactate, though because B. bifidum is a less efficient consumer of HMOs, it likely produces less of these products than B. infantis.

See full infographic: WEB | PDF

Benefits of a Bifidobacterium

The decline of Bifidobacterium in infant gut microbiomes and the associated dysregulation of the microbial community, with more numerous potential pathogens, has been suggested as one possible contributor to the increased incidence of autoimmune diseases that plague residents of resource-rich nations. Conversely, observational studies have shown beneficial immune effects of having a fecal microbiome dominated by Bifidobacterium. In two studies in Bangladeshi infants and young children, fecal B. infantis and Bifidobacterium abundances at two months of age were strongly correlated with improved vaccine responses at six months and two years old compared with infants not colonized by B. infantis or with low relative abundances of Bifidobacterium.

Additionally, bifidobacteria are less likely than other microbes, especially potential pathogens, to carry and share antimicrobial resistance genes, which can lead to a higher risk of antibiotic-resistant infections. In an observational study of Bangladeshi and Swedish infants, a dominance of intestinal Bifidobacterium was associated with a significant reduction in both the number and the abundance of antibiotic resistance genes. Moreover, compared with matched-control breastfed infants, supplementation with B. infantis EVC001 led to a reduction of antibiotic resistance genes by 90 percent, a drop largely driven by a reduction in levels of Escherichia, Clostridium, and Staphylococcus—potentially pathogenic bacteria that play a major role in the evolution and dissemination of antibiotic resistance genes.

In an effort to restore the Bifidobacterium-dominated infant gut microbiome that was typical of breastfed babies 100 years ago, we decided to conduct a randomized, controlled trial using the B. infantis EVC001 probiotic. Given that not all B. infantis strains consume all HMOs efficiently, we selected B. infantis EVC001 because we knew this strain had the full cassette of genes needed to fully digest all HMOs. Healthy, full-term, breastfed infants were randomized to consume B. infantis EVC001 for 21 consecutive days starting on day 7 postnatal or to not receive the probiotic.

A PROBIOTIC THAT STICKS: Scanning electron micrographs of infant fecal samples show a large increase in the number of Bifidobacterium microbes in those treated with a probiotic called EVC001 (right) compared with controls (left).

PEDIATR RES, 86:749–57, 2019

Compared with breastfed control infants who did not receive the probiotic, supplementation resulted in a 10,000,000-fold average increase in levels of fecal B. infantis and increased fecal Bifidobacterium by 79 percent during the supplementation period, and this was still true at one month post supplementation. This means Bifidobacterium colonization persisted without the continuation of probiotic supplementation. Additionally, colonization of B. infantis persisted until one year of age if infants were continuing to consume any breast milk and were not exposed to antibiotics. Importantly, the supplemented infants exhibited an 80 percent reduction in potential gut pathogens belonging to the families Enterobacteriaceae and Clostridiaceae and reduced fecal endotoxin. Additionally, we saw a 2-fold increase in fecal lactate and acetate and a 10-fold decrease in fecal pH. The supplemented infants’ gut microbiomes and biochemistry resembled norms observed a century ago.

We also identified some clues about the consequences of the gut microbiome’s “modernization.” Breastfed infants with low fecal Bifidobacterium had excreted 10-fold more HMOs in their stool throughout the two-month study period than infants supplemented with B. infantis EVC001, indicating that HMOs—the third most abundant component in breast milk—were going to waste. We also found that infants with low fecal Bifidobacterium had several-fold higher levels of fecal
proinflammatory cytokines compared with infants whose gut microbiomes were dominated by Bifidobacterium post supplementation with B. infantis EVC001.

Taken together, these data demonstrate that this particular strain of B. infantis, provided as a probiotic to breastfed infants, dramatically colonized the infant gut microbiome during and after supplementation, and beneficially remodeled the microbial, biochemical, and immunological environment in the infant gut. Many infants around the world never acquire B. infantis, but the combination of breastfeeding and probiotic supplementation with this bacterium seems to lead to a nourishing and protective gut environment.

Many infants around the world never acquire B. infantis, but the combination of breastfeeding and probiotic supplementation with this bacterium seems to lead to a nourishing and protective gut environment.

Our findings also support the hypothesis that the ineffectiveness of some probiotics in adults is due in part to the fact that they are introducing a new species to an established community with few ecological niches still open. Probiotics may not work in infants when there is a mismatch between the carbohydrate needs of the probiotic and the availability of highly specific carbohydrates such as HMOs in breast milk. Because B. infantis efficiently consumes almost all HMOs found in breast milk, it is likely to find an open ecological niche and then outcompete other microbes, especially proinflammatory pathogens.

Many scientists are working to understand what the infant gut microbiome really means for health across the lifespan. Meanwhile, we are turning our attention to other questions: How do colonization patterns of Bifidobacterium differ in infant populations around the world from infancy to weaning? And what solid foods support a healthy gut and immune system? Working with funding from the National Institutes of Health, we are now conducting a study designed to understand how the carbohydrate structures of complementary foods influence microbial function that will support a healthy gut microbiome and immune system development in late infancy and early toddlerhood. The ultimate goal is to identify specific carbohydrate structures in the diet that selectively feed beneficial gut microbes in children during the critical window of immune development for lifelong health.

Jennifer Smilowitz is the associate director of the Human Studies Research Program at the Foods for Health Institute and a research scientist in the Department of Food Science and Technology at the University of California, Davis. Diana Hazard Taft is a postdoctoral research fellow in David Mills’s lab in the Department of Food Science and Technology and a member of the Foods for Health Institute at UC Davis.