Pathogenic microbiome bacteria change shape to adapt to nasopharyngeal environment

Microbiome bacteria are highly adapted to their surroundings.  They face constant pressure from the immune system as well as other bacteria, fungi, and even small molecules such as antibiotics.  It should come as no surprise then, that many of these bacteria have undergone major evolutionary adaptations to survive the human body.  Apparently, as discovered by French group and published in PLoS Genetics, one common strategy amongst many different bacteria is a shift from rod shaped to spherical shaped (coccoid). 

The scientists investigated the genealogy of bacteria for the family Neisseriaceae, which have species with a high diversity of shapes, including some members from the human nasal microbiome, like Neisseria meningitidis that are spherical.  In tracing the histories of this bug they noted that many other bacterial species showed a similar tendency, that is they converted from rod to coccoid after entering the nose.  The researchers were even able to track down the simple genetic mutations responsible, and they noted that this mutation to coccoid conferred many fitness advantages over the rod shape.  For example, the coccus shape has a higher surface to volume ratio than the rod, so that the host immune system has less surface to detect, without sacrificing as much volume in the cell.

It is interesting to look into the evolutionary developments of microbiome bacteria, because they shed light on the shared strategies of these commensals in coexisting with their host.  These adaptations actually differentiate the commensals from the non-commensals which are potentially pathogenic, because foreign bacteria don’t stand a chance of evading our immune system, especially compared to bacteria that have evolved with us throughout the entirety of human history. 

The nasal microbiome of infants may impact risk of developing asthma

Many lower respiratory illnesses have been shown to associate with specific lung, throat and nasal bacteria, but the role of the microbiome is still unclear, and mechanisms for the connection have yet to be proven.  Of particular interest is asthma, which affects around 7% of people in the US, and increases a person’s risk for many other conditions.  While it is normally diagnosed in toddlers, scientists believe that the groundwork for the disease is actually laid during infancy.  With that in mind, researchers in Australia performed the first longitudinal study of infants’ nasopharyngeal (nose and throat) during the first year of their lives, and tracked episodes of respiratory illness during that time.  They discovered a strong connection between the microbiome and respiratory illness, including asthma, and last month published their results in Cell Host and Microbe.

The researchers collected nasopharyngeal microbiome samples from 234 infants at different time points during their first year of life.  Most infants’ microbiomes were dominated by the following species: Moraxella catarrhalis, Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, and Alloiococcus otitidis.  Interestingly, this was true for infants regardless of birth delivery mode (i.e. cesarean or vaginal) as well as length of breast feeding.  In contrast, having a furry animal in the house tended to increase the abundance of Streptococcus, but having older siblings tended to decrease it.  In addition, there were strong seasonal effects on the microbiome, with Haemophilus being associated with the summer, and Moraxella the winter.  In children with respiratory illness, Haemophilus, Moraxella, and Streptococcus were most frequently measured, and Staphylococcus, Alloiococcus, and Corynebacterium least frequently measured.

When the scientists compared their results with the asthma outcomes of the children at 5 years old they noticed one significant trend.  Colonization by Streptococcus at around 2 months old, which was asymptomatic at the time and occurred in 14% of infants tested, was strongly connected to chronic wheezing (itself an indication of asthma) at 5 years old.  They suggest that the developing airways in infants may be especially vulnerable to Streptococcus.

This long term study does a really nice job of defining how the microbiome grows and develops in the airways of infants – something which previously hadn’t been performed at such a large scale.  While this study alone does not figure out exactly what the microbiome’s role is in childhood respiratory illnesses, it does provide a baseline for future studies to work off of.