Novel combination of techniques improves identification of soil bacteria involved in wood decomposition: The latest from Mohn lab

In a bid to overcome the limitations of what scientists found previously from culture-dependent studies, new research shows stable isotope probing, coupled with next-generation sequencing techniques, can be used to identify which organisms living in the complex microbial soil community are involved in the decomposition of lignin, cellulose, and hemicellulose–three major polymers that make up wood.

Researchers from the lab of Bill Mohn (Microbiome Insights co-founder) at University of British Colombia labelled the lignin, cellulose, and hemicellulose of wood samples with a carbon isotope and allowed the process of decomposition to proceed in experimental microcosms. Subsequent amplicon and shotgun sequencing of the microbial communities in the microcosms: first, identified the organisms present without the use of cultures; and second, by measuring the total assimilation of the carbon isotope into the DNA of the sequenced amplicons, identified which species were involved in decomposition. This method greatly improves the understanding of the species and genes involved in this essential process — an insight not possible with standard culturing methods.

Forest soil decomposition of wood is a major global carbon sink, making it important for the study of climate change. To date, researchers knew microbes must be involved in helping fungi, the main drivers of wood decomposition, in the task of recycling this material but were limited in the ability to identify those involved.  This was mostly due to the fact that many bacteria cannot be grown on cultures in the lab. This new approach not only removes this barrier but also, due to the ability of metagenomics to work with pooled samples, provides a glimpse of the entire community in the sample —providing a more natural representation of the forest communities.

The researchers found that bacteria, specifically Gram-negative types from the families Comamonadaceae and Caulobacteraceae, were more involved in lignin degradation, with fungi taking on a prominent cellulose degrading role. Interestingly too, most species incorporated a carbon label from a single lignocellulosic polymer, strongly suggesting specialization among the microbes involved.  Furthermore, they found that variations in the community compositions across different soil types and soil layers constrained the degrading activity. According to the researchers involved: “the relationship between these communities and process rates should receive continuing study to refine our understanding of soil carbon stabilization and terrestrial carbon cycling models.” Additionally, the newly discovered sets of  gene clusters involved in the degradation process provide “a trove of potentially novel enzymes for biotechnological applications.”

This study was recently covered in Chemistry World.


New paper from Microbiome Insights co-founder on critical window for the gut microbiome in infants and the later occurrence of asthma

Among serious and chronic childhood diseases, asthma is the most prevalent. Currently there exists no cure for asthma—only treatments designed to help manage symptoms. Recently, a body of research attempting to unravel how this condition develops  in young children has emerged, so that prevention may one day eliminate or reduce the burden of this chronic condition.

Recent work identified the existence of a critical window during the early lives of both mice and children, during which gut microbial changes are associated with the development of asthma. This provided an avenue to explore the role of the gut microbiome during early childhood development and the onset of chronic diseases like asthma. Importantly though, we know the gut microbiome varies greatly among those raised in different geographic regions. Therefore, understanding how changes in gut microbiota related to asthma development differ globally may provide valuable insights into the mechanism of asthma development.

A new paper, led by Microbiome Insights co-founder Brett Finlay and published in The Journal of Allergy and Clinical Immunology, evaluated the associations of fungal and bacterial changes (dysbiosis) in infants raised in the non-industrialized setting of rural Ecuador. The research was conducted as a collaboration between members of the Universities of British Colombia and Calgary, the BC Children’s Hospital, and Universidad Internacional del Ecuador. Children with atopic wheeze (27 in total) along with 70 healthy controls were identified and their bacterial and eukaryotic gut microbiota analysed at age 3 months. Stool samples were collected and sequencing of the 16S and 18S regions predicted bacterial metagenomes while fecal short chain fatty acids were determined via gas chromatography.

Results indicated that, similar to the previous findings in Canadian children, microbial dysbiosis in Ecuadorian infants at 3 months was associated with the subsequent development of atopic wheeze. Surprisingly though, the dysbiosis observed in Ecuador involved different bacteria taxa as well as some fungal species, and this was more pronounced than in Canada. Some predictions based on the metagenome analysis also emphasized significant dysbiosis-associated differences in genes involved in carbohydrate and taurine metabolism. The fecal short-chain fatty acid acetate was reduced while caproate was increased in children at 3 months who later developed atopic wheeze.

This work continues to provide evidence that there is a critical window during the first 100 days of life during which microbial dysbiosis is strongly associated with development of atopic wheeze. The study also yielded several valuable pieces of information. Despite the involvement of different bacteria taxa, both the Canadian and Ecuadorian populations had decreased fecal acetate, suggesting alterations to fermentation patterns may be a common factor associated with atopic wheeze. Furthermore, the pronounced role of fungal dysbiosis in this study led researchers to recommend that “the role of P. kudriavzevii and other yeasts should be explored in mechanistic studies using animal models.”

Along with more studies characterizing the early microbiome in more communities around the world, optimized biomarker studies of microbial taxa and metabolites could lead to better predictions of risk and therapeutic strategies to restore gut microbial health as a prevention method.


Microbiome Research: Don’t Forget The Fungi

Microbial Interactions In Living Systems

The emerging field of the microbiome is in pursuit of understanding the microbe-microbe and microbe-host interactions that occur in virtually all living systems. This includes interactions critical to plant and animal health. The fundamental question is: What role(s) do the microbes and their functions play in broader systems?

Advancements in technology, such as next generation sequencing, have allowed us to overcome the barriers of culture-dependent methods of identification and classification, providing the ability to sequence and identify a more complete community of microbes in any given sample with a high degree of sensitivity and reproducibility.

It seems, however, that the term ‘microbiome’ tends to implicitly refer to commensal and pathogenic bacteria, with very little attention paid to the role of eukaryotic organisms. As such, the field is heavily utilizing 16S amplicon sequencing to increase our understanding of these bacteria. But what about other amplicons such as 18S or ITS (internal transcribed spacer) that shed light on eukaryotic or fungal communities?

Penicillium, ascomycetous fungi of major importance

The Mycobiome

In recent years, there have been more published data elucidating the presence and contribution of fungi in certain disease states. These fungi have been shown to interact with bacterial communities in either a synergistic or competitive manner. In either relationship, these fungi may be a critical component of the progression of such diseases—including hepatitis B, cystic fibrosis, and even inflammatory bowel disease. As a result, researchers have coined the term ‘mycobiome’ to refer to the communities of fungi that may play an interesting role in the system.

The human body is a unique ecosystem, and we have long known mucosal sites are abundant with fungal flora.  What we are beginning to identify is how these communities interact with other sites across the body, where bacterial communities reside. Besides the specific diseases associated with fungi, we are seeing evidence that overall gut health is maintained by a degree of fungal-bacterial interaction. Mechanistically, the mycobiome appears to play a role in inflammation and metabolism by modulating the bacterial microbiome.

Environmental microbiomes are also of growing interest in the microbiome field, with a particular focus on ocean microbiomes, air pollutants, and soil microbiomes. In soil microbiomes, where fungi are prevalent, researchers are interested in certain subcategories; studies focus on the soil microbiome, the plant/rhizosphere microbiome, or the point at which these two microbiomes interact, which is called the mycorrhizosphere. The fungal component of these microbial communities plays a critical role in the nutrition and growth of plants as well as in the exclusion of plant diseases. Mycorrhizal fungi have even been shown to mediate signaling between plants.

Amplicon Sequencing: 16S, 18S, & ITS

Unlike other next generation sequencing labs that have exclusively focused on the approaches of molecular biology and genomics, Microbiome Insights also pulls from expertise in microbial ecology and infectious disease to provide a more complete picture of the ecosystem. We have implemented standardized protocols for 16S (Prokaryotic) sequencing and have developed robust workflows for both 18S (Eukaryotic) and ITS2 (fungal) sequencing using the Illumina Miseq.  We apply these approaches as necessary to address specific scientific questions, and can build on this data using shotgun metagenomic sequencing. Altogether our expertise allows us to provide our customers with a full suite of tests—without forgetting the fungi.