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Nice write-up of how what happens from the type of birth (vaginal vs cesarean) affects the baby's microbiome (community of microbes). Remember, it is very complicated and much is still unknown. (UPDATE: see January 16, 2015 post discussing research by Dr. Dominguez-Bello who is conducting a study in which babies born via C-section are immediately swabbed with their mother's vaginal secretions; these babies will then be followed for years). From Gastroenterology and Endoscopy News:

Delivery Mode Alters Newborn’s First Bacterial Exposure

 A baby’s first exposure to bacteria varies by the method of delivery, researchers have foundThese differences could have health implications later in life, according to an emerging body of evidence that suggests gut bacteria may be important to the development of a healthy immune system (Arrieta MC et al.Front Immunol 2014;5:427). For example, evidence shows that alterations in gut bacteria early in life may increase the incidence of allergies later on (Bendiks M, Kopp MV. Curr Allergy Asthma Rep 2013;13:487-494).

In the new study, presented at the 2014 annual meeting of the North American Society for Pediatric Gastroenterology, Hepatology and Nutrition, a group at the University of Colorado School of Medicine, in Aurora, compared oropharyngeal aspirates taken from 12 infants born by cesarean delivery and 11 born vaginally, and their bacterial content by sequencing the bacterial genes in the samples (abstract 7). Samples taken from the mothers’ vaginal and rectal areas, and samples of the infants’ stool, were also analyzed for bacterial genes.

Bacteria in aspirates from newborns delivered vaginally were more similar to the bacteria found in samples from their mothers than the aspirates from infants born by cesarean delivery, the investigators found. Infants born vaginally had higher numbers of firmicutes (62.6% vs. 30.1%; P=0.0013), particularly lactobacilli typically found in the vagina.

Aspirates from infants born by cesarean delivery, in contrast, had higher levels of Actinobacteria (20.1% vs. 3.8%; P=0.045), which are found on the skin. Stool samples from vaginally delivered newborns also had greater numbers of Bacteroidetes than stool samples from infants born by cesarean delivery. This difference persisted through six weeks of life, the researchers said.

David Brumbaugh, MD, assistant professor of pediatrics at the University of Colorado School of Medicine, in Aurora, said the finding of fewer Bacteroidetes in cesarean newborns is potentially alarming. Studies of mice raised in sterile conditions have shown that exposure to a specific type of Bacteroidetes, Bacteroides fragilis, suppresses the animals’ inflammatory response (Mazmanian SK et al. Nature 2008;453:620-625), he said. 

“The fact that this bacteria never gets established early in life [in babies born by cesarean delivery] is concerning,” he said. Some studies have suggested that infants born by cesarean delivery may be at greater risk for developing conditions such as asthma, type 1 diabetes and celiac disease (Cho CE, Norman M. Am J Obstet Gynecol 2013;208:249-254). But not all studies have supported such risks; other studies suggest that genetic factors or the reason for the cesarean delivery itself may contribute to disease later in the child’s life (Almqvist C et al.Clin Exp Allergy 2012;42:1369-1376).

Jean-Eric Ghia, PhD, assistant professor of immunology and internal medicine at the University of Manitoba, in Winnipeg, Canada, said the findings add to a body of evidence suggesting that gut bacterial colonization is affected by mode of delivery, and these altered gut bacteria might contribute to immune system–related disease later in life (Neu J, Rushing J.Clin Perinatol 2011;38:321-331). “The first colonization of the gut happens when the baby comes out,” he said. But he noted that long-term studies are needed to assess the effect of these gut differences on health in the long term. He noted that a multitude of exposures before and after birth can also influence gut biota (Munyaka PM et al. Front Pediatr. doi:10.3389/fped.2014.00109 [published online October 9, 2014]). “It’s really, really complicated,” he said.

An interesting small study of the human armpit bacterial community. From Real Clear Science:

Antiperspirants Alter Your Armpit Bacteria and Could Actually Make You Smell Worse

In modern society, antiperspirants are widely hailed as a godsend, dispelling the inconvenient odors wafting from armpits everywhere. But a new study casts doubts on their vaunted position. As it turns out, antiperspirants may actually make you smell worse in the long run.

For 90% of all Americans, slathering on deodorants and antiperspirants is a daily occurrence, a precautionary measure against foul odors and unsightly sweat stains. The odors arise when bacteria living in our armpits break down lipids and amino acids excreted in sweat into more smelly substances. Deodorants employ antimicrobial agents that kill off bacteria, as well as chemicals that replace noxious odors with pleasant aromas. Deodorants that double as antiperspirants, like Degree, Old Spice, and Dove, take the process one step further by physically plugging sweat glands with aluminum-based compounds.

While most of us might only concern ourselves with the dry, aromatic benefits of antiperspirants and deodorants, researchers at the Laboratory of Microbial Ecology and Technology at the University of Ghent in Belgium are more interested in the effects on bacteria. Billions of bacteria dwell in the "rain forests" under our arms, and the substances we don are mucking with their habitats!

To uncover how deodorants and antiperspirants affect armpit bacteria, Chris Callewaert, a Ph.D student specializing in microbial ecology, and a team of researchers recruited eight subjects for a task a great many people (and especially their friends) might deem unbearable: Six males and two females pledged not to use deodorant or antiperspirant for an entire month. Specifically, four subjects stopped using their deodorants and another four stopped using their antiperspirant deodorant. (Most antiperspirants are also deodorants. See image below for an example.) Another control subject who did not regularly use either was asked to use deodorant for a month. The duration was chosen because it takes approximately 28 days for a new layer of skin cells to form.

The researchers analyzed the diversity and abundance of subjects' armpit bacteria at various timepoints before they stopped using antiperspirant, during the period of abstaining from antiperspirant, and for a few weeks after resuming the use of antiperspirant. Switching hygiene habits plainly altered the armpit bacterial communities of every subject. Since no two armpits and their resident bacteria are identical, it was difficult to pinpoint precise changes brought about by deodorants or antiperspirants, but one clear trend did materialize: antiperspirants resulted in a clear increase of Actinobacteria.

You might not recognize the name of Actinobacteria, but chances are, you've smelled them. Dominated by Corynebacterium, they are the major instigators of noxious armpit odor. Other microbes that inhabit the armpit, like Firmicutes and Staphylococcus, don't produce odors as quickly, nor are those odors nearly as pungent.

Callewaert believes the aluminum compounds in antiperspirants may be to blame, killing off "good," less smelly bacteria and allowing "bad" bacteria to dominate. His study found that deodorants which lack these sweat-blocking antiperspirant compounds are actually linked to a slight decrease of stinky Actinobacteria.

Though antiperspirants and deodorants are widely used, they are only a temporary fix."The measures we utilize today do not take away the initial source: the odor causing bacteria," Callewaert told RealClearScience. "Deodorants only mask unpleasant odors. We can do better than that. The follow up of this research is finding better solutions."

And Callewaert is already working on one: "armpit bacterial transplantation"."We take away the bad bacteria from the armpit of somebody with a body odor, and replace it with the good bacteria of a relative who doesn't have a body odor," he explained."So far we have helped over 15 people. For most subjects it brings immediate improvements. Most of them on a permanent time scale, although there are also people who suffer again from a body odor after some months."

Two related articles, the first from a month ago, but both discuss eating fresh foods of summer and the effect on the microbiota. From Gut Microbiota Worldwatch:

Seasonal diet changes affect the composition of our gut microbiota

The mix of bacteria that live in our gut changes throughout the year, to match the food we eat in every specific season. For example, bacteria that process fresh fruit and vegetables are more abundant in the summer, and those that process fats are mode abundant in winter times. A group of scientists at the University of Chicago has found evidence of this seasonal shift in the gut flora, by studying the remote Hutterite population, in North America. The traditional diet and common meals of this community have allowed researchers to study the effect of one common diet in a large population over a long period of time.

Hutterites live in communal farms (colonies) and eat meals in common dining rooms, using traditional recipes that have been relatively stable over time and between colonies. They have little contact with the world outside their colonies, which translates into a very homogeneous genetic pool. Sixty Hutterites from six colonies answered questionnaires about what they ate over the course of a year. During the same period, scientists sampled their stool periodically, to find the genetic sequences of bacteria contained in their gut.

The Hutterites’ diet is relatively stable, except that in summer they eat more fresh fruit and vegetables, and in winter they eat less, and turn to frozen or canned food. Remarkably, their gut flora responded to these changes with massive modification in the abundance of certain bacteria. For example, during summer Bacteroidetes were more abundant: this group of bacteria contain complex carbohydrate digesters, which may be at work in processing fresh fruit and vegetables.

On the other hand Actinobacteria increased in winter: these microbes are associated with processing fat, and with a decreased content of fibre in food. Researchers also found seasonal shifts in other types of bacteria, whose associations with food are still unknown. Notably, the trends were almost identical in all six colonies, possibly a result of a very homogenous lifestyle carried on in a very similar environment.

Although Hutterites live in a relatively isolated way, they use technology and medicine, which makes their lifestyle closer to the general population than that of other more traditional communities. That is why the authors believe that these results may be extended to the general population.

This healthy living article promotes eating fresh fruits and vegetables (tomatoes, blueberries, asparagus, and leeks) as good for the gut microbiome. From Huffington Post:

4 Summer Foods That Can Help Trim Your Waist