Nav: Home

Childhood antibiotic treatments reduce diversity and stability of intestinal microbiota

June 22, 2016

The DIABIMMUNE project followed the development of 39 Finnish infants from birth to the age of three. Half of the children received 9-15 antibiotic treatments during the research period, and the other half did not receive any such treatments. Stool samples were collected from the children monthly between the ages of 2 and 36 months, for a total of 1069 samples. The study involved researchers from Aalto University, the University of Helsinki, Helsinki University Hospital and the Broad Institute of MIT and Harvard.

'We found that the microbial community of antibiotic-treated children is less stable and less diverse. Interestingly, this is most noticeable on the strain level, where children who received multiple antibiotic treatments had many more single-strain species, whereas children who never got any antibiotics had more diverse species, with multiple strains for each species' explains Dr. Moran Yassour, a postdoctoral fellow at Professor Ramnik Xavier's group at the Broad Institute of MIT and Harvard Yassour.

The problem of unnecessary antibiotic treatments

With every passing generation, important species of intestinal bacteria seem to be disappearing due to the effects of antibiotics. The discovery of antibiotic compounds has transformed the medical practice, and antibiotic treatments save lives on a daily basis. At the same time, antibiotics are still being unnecessarily prescribed to children, for example against viral infections, and this study highlights the consequences of repeated antibiotic treatments on the developing infant gut microbiome.

'Treatments, such as antibiotics, that have an effect on early childhood microbial populations can make children prone to long-term illnesses that manifest themselves later on, such as asthma, inflammatory bowel diseases, diabetes and obesity. Antibiotic treatments should in future be more precisely focused against the infections preceding the treatment,' says Professor Mikael Knip from the Children's Hospital and the University of Helsinki, who is leading the DIABIMMUNE research project.

The type of birth also affects the development of a child's intestinal microbiomes. The intestinal microbiomes of children born by caesarean (C) section are usually not as diverse of those that undergo a vaginal birth, and are characterized by the lower abundance of various Bacteroides species in the first 6 months of life. The microbiomes also significantly develop and establish themselves during a child's first months of life, with the composition of microbiota taking its stable adulthood composition during the child's third year. The intestinal microbiota has a significant effect on the development of a child's immunity. A healthy, diverse, and stable microbiota have been shown to promote health: they promote absorption of nutrients, support the metabolism and protect from infections.

'Like in previous studies, we also observe a very strong impact of delivery mode on the infant gut microbiome. The gut microbial signature of children born by C-section is very unique, as none of the Bacteroides species are detected in the first 6-18 months of life. Surprisingly, 20% of vaginally born children displayed a similar 'low-Bacteroides' signature, an observation that has not been previously reported. We have searched extensively for clinical variables that may explain this observation, yet the numbers are too small to find statistically significant direct associations.' Dr. Yassour notes.

In the long-term, the microbial diversity of all children with the 'low-Bacteroides' signature remained lower, regardless of their delivery mode.

Antibiotic-resistant bacteria

Often-repeated antibiotic treatments given during early childhood interfere with the development of the intestinal microbiota and lead to the development and possible spread of antibiotic-resistant microbe populations. Researchers observed a rapid increase in antibiotic resistance genes--genes that convey bacterial resistance to antibiotics--after antibiotic treatments. This increase was usually short-term, followed by a rapid decrease in the abundance of the resistance genes in the following month. On the other hand, resistance genes found on mobile elements - that transfer more easily between bacteria - sometimes remained in the intestines for significantly longer periods of time.

'If the intestinal microbiota is healthy, the resistant bacteria are not usually able to multiply because they do not find a niche in the ecology. However, during antibiotic treatment other bacteria are killed and resistant bacteria can proliferate freely. There is also the risk that certain pathogens gain resistance implicating that the diseases caused by them will become very hard to treat. This is what is being referred when people talk of hospital bacteria,' explains doctoral candidate Tommi Vatanen from the Aalto University Department of Computer Science and the Broad Institute in Cambridge, USA.

'The strength of this study lies in its unique combination of longitudinal monthly samples coupled with deep metagenomic sequencing. These were key for both the identification of strains, and quantification of antibiotic resistance genes,' Dr. Yassour emphasizes.

The study has been funded primarily by the EU (7th framework programme), the Finnish Academy and the Juvenile Diabetes Research Foundation. The research results have been published in the internationally recognised publication series Science Translational Medicine, and were featured on the issue's cover.
More information:
Tommi Vatanen
Doctoral Candidate
Aalto University, Department of Computer Science and Broad Institute
Tel. +1-857-498-4141

Mikael Knip
Children's Hospital, University of Helsinki and Helsinki University Hospital
Tel. +358504487722

Moran Yassour
The Broad Institute of MIT and Harvard
phone: +1 (617) 714-7358


Aalto University

Related Bacteria Articles:

Bacteria must be 'stressed out' to divide
Bacterial cell division is controlled by both enzymatic activity and mechanical forces, which work together to control its timing and location, a new study from EPFL finds.
How bees live with bacteria
More than 90 percent of all bee species are not organized in colonies, but fight their way through life alone.
The bacteria building your baby
Australian researchers have laid to rest a longstanding controversy: is the womb sterile?
Detecting bacteria in space
A new genomic approach provides a glimpse into the diverse bacterial ecosystem on the International Space Station.
Hopping bacteria
Scientists have long known that key models of bacterial movement in real-world conditions are flawed.
Bacteria uses viral weapon against other bacteria
Bacterial cells use both a virus -- traditionally thought to be an enemy -- and a prehistoric viral protein to kill other bacteria that competes with it for food according to an international team of researchers who believe this has potential implications for future infectious disease treatment.
Drug diversity in bacteria
Bacteria produce a cocktail of various bioactive natural products in order to survive in hostile environments with competing (micro)organisms.
Bacteria walk (a bit) like we do
EPFL biophysicists have been able to directly study the way bacteria move on surfaces, revealing a molecular machinery reminiscent of motor reflexes.
Using bacteria to create a water filter that kills bacteria
Engineers have created a bacteria-filtering membrane using graphene oxide and bacterial nanocellulose.
Probiotics are not always 'good bacteria'
Researchers from the Cockrell School of Engineering were able to shed light on a part of the human body - the digestive system -- where many questions remain unanswered.
More Bacteria News and Bacteria Current Events

Top Science Podcasts

We have hand picked the top science podcasts of 2019.
Now Playing: TED Radio Hour

Why do we revere risk-takers, even when their actions terrify us? Why are some better at taking risks than others? This hour, TED speakers explore the alluring, dangerous, and calculated sides of risk. Guests include professional rock climber Alex Honnold, economist Mariana Mazzucato, psychology researcher Kashfia Rahman, structural engineer and bridge designer Ian Firth, and risk intelligence expert Dylan Evans.
Now Playing: Science for the People

#541 Wayfinding
These days when we want to know where we are or how to get where we want to go, most of us will pull out a smart phone with a built-in GPS and map app. Some of us old timers might still use an old school paper map from time to time. But we didn't always used to lean so heavily on maps and technology, and in some remote places of the world some people still navigate and wayfind their way without the aid of these tools... and in some cases do better without them. This week, host Rachelle Saunders...
Now Playing: Radiolab

Dolly Parton's America: Neon Moss
Today on Radiolab, we're bringing you the fourth episode of Jad's special series, Dolly Parton's America. In this episode, Jad goes back up the mountain to visit Dolly's actual Tennessee mountain home, where she tells stories about her first trips out of the holler. Back on the mountaintop, standing under the rain by the Little Pigeon River, the trip triggers memories of Jad's first visit to his father's childhood home, and opens the gateway to dizzying stories of music and migration. Support Radiolab today at