One of Dr. Janet Jansson’s many ongoing projects, and a big focus in microbiology over the last few years has been the study of the human gut microbiome. As ASM 2010 draws near, you can be sure that human microbiome research is an area that will get a lot of attention.

I thought it would be a good time to review a human microbiota paper for all our readers. As an introduction to our guest speaker at our ASM Workshop on Monday, May 24th, this article discusses  Dr. Jansson’s 2007 study titled: “Molecular Fingerprinting of the Fecal Microbiota of Children Raised According to Differet Lifestyles“, from AEM, vol. 73, No.7, p.2284-2289.

Introduction:

The human intestinal community is very unique to each individual. While it doesn’t change much, with the exception of when antibiotics are used, the gut flora is quite stable and is heavily dependent on diet and lifestyle.

To gain a better understanding of the effects of diet and lifestyle on the human gut microbiota, this study looked at fecal microbial communities in children raised with two different types of diets. The first group of kids were living farm life,  consumming unpasteurized dairy products and home grown food and having frequent contact with farm animals.

The second group of kids were raised following an anthroposophic lifestyle, which means that their diet consisted of organically produced foods and vegetables were preserved by fermentation with lactobacilli. These children tended to be breast fed longer than average children. In addition, these kids did not receive antibiotics as much and their parents avoided vaccinations such as with MMR.

To determine the differences in the microbial populations of these groups of children who were between the ages of 5 and 13 years, the authors used T-RFLP analysis after isolation of the DNA from fecal samples using the UltraClean Soil DNA Isolation Kit combined with high powered bead beating. The fecal microbiota of 90 children who were either living on farms or attending Steiner schools (kids living the anthroposophic lifestyle ) were from Germany, Sweden, and Switzerland.

Methods:

Children did not have antibiotics during the last 3 months and were not ill at the time of sampling. Of the 90 children, 23 were anthroposophic kids, 19 were controls- kids living in the same area but attending public schools, 26 kids were living on farms and 22 control kids were not living on farms but in the same area.

DNA was isolated from fecal samples and T-RFLP performed for 16 s rRNA for total bacteria and also for lactic acid bacteria (LAB). The 16s rRNA genes were also cloned and sequenced to confirm identities of bacterial species that dominated in some of the children.

Results:

A total of 140 different TRFs were identified and each individual had a unique profile. Only a very small number of TRFs were common to all subjects. There was no clustering with regards to lifestyle, sex, diet, or origin. Of the predominant TRFs, the genera Eubacterium and Clostridium were the most common (90/90 and 89/90) respectively.

The Steiner children had more diversity in their fecal bacteria compared to farm children while the farm children had higher abundancies of some TRFs. Based on the data and questionnaires, the consumption of organically produced food correlated with high diversity while high consumption of farm milk correlated with low diversity. Children who never used antibiotics had higher diversity, as expected, while children who received the MMR vaccine showed lower diversity.

Using the LAB primers to assess the differences in commensal gut microbiota, one of the dominant clones, TRF 250, was unclassifiable below the phylum level, with the closest match to Clostridium ramosum (88%). This clone appeared in 57/82 individuals in the Steiner children and the reference groups but not the farm children. This particular phylotype may play an important role in the gut microbiotic environment given its dominance in the higher gut diversity children.

Conclusions:

Every individual has their own very specific gut microbiome.  No two samples are alike.  However, there are some predominat species that may be higher or lower in individuals based on diet.

This study found that a difference existed in the gut microbiota of children based on their lifestyle which did not relate to the geographic origin, as some other studies have observed. The Steiner children, who were from Sweden, Germany, and Switzerland, ate organically grown foods and foods fermented with lactobacillus as a preservative, had a higher diversity of bacteria. These kids in general do not get vaccinated and avoid antibiotics. The farm raised children had lower diversity but higher overall abundancies of gut microbes.

Is high diversity better? Higher diversity of gut microflora is considered better because it allows for better resilience in fighting infection or during disturbances.  For example, it has been previously reported that patients with Crohn’s disease have lower gut microbial  diversity, suggesting a link to human health. In the present study, farm children had the lowest diversity although they have also been shown to have a lower rate of developing allergies, supporting the hypothesis by Ley, RE, et al (2006), that “keystone species” can alleviate the requirement for higher diversity.

Of the Lactobacillus biota, one clone of interest, TRF 250, was predominant in all the kids except the farm raised children. This sequence does not match with any significant similarity to any known organism below the phylum level.  More clarity on the phylogeny and function of this organism could lead to more answers in the search for understanding the difference in human intestinal health.

Summary:

This interesting research demonstrates how much more we can know and ask about the human microbiome. Every discovery leads to many more questions.  The identification of healthy and disease gut microbiota over the next decade of microbiology research will allow us to understand the cause and effects of many diseases, including colon cancer. I am looking forward to hearing about the progress and interesting finding by many more of the human microbiome researchers this year at ASM 2010.

~Suzanne

See you at ASM Booth 1020. Come chat with us over food and drinks at our workshop at ASM Monday evening, the 24th. We look forward to meeting you and hearing your thoughts on what we can do better and how we can aid your research.