Appreciating the full scale of human microbiome research
The human microbiome has mushroomed from a little-known, niche field within microbiology into a rapidly evolving and expansive research area of its own. This explosion has been driven by the availability of scalable nucleic acid extraction kits, low-cost next-generation sequencing (NGS) platforms, and robust bioinformatics pipelines. Consequently, it has provided deep insights into the complexities of microbial communities.
Not surprisingly, microbiome research has focused primarily on human physiology. The human gut and skin have their own unique microbiomes. They deconvolute the core microbial constituents, and their functions. As a result, it has given researchers a view into their effect on human physiology. It’s now well-accepted that there are three to 10 times more bacterial cells than human cells on and in our bodies, consisting of more than 10,000 distinct species of bacteria.1,2 The human body has, appropriately, been equated to an elaborate culturing flask built for the growth of intricate microbial communities.3
There has been a ton of research on the biomedical role of human microbiome. The magnitude of research has grown, to a planetary scale. Initiatives like the Earth Microbiome Project (EMP) is tackling questions about free-living and host-associated microbiomes, in a wide range of environments and geographies.4 The EMP and projects like it have revealed so much about these invisible communities, their dynamics, and how they are driving macro changes to our planet and its inhabitants.
To get a better appreciation of the full scope and scale of human microbiome research and beyond, here’s a roundup of some interesting microbiome publications. This video will surely make you exclaim, “The microbiome does WHAT?”
Watch Video: From underground to outer space: Dr. Christopher Mason’s Microbiome Journey
Characterizing the infant gut microbiome
A lot of human gut microbiome research focuses on the microbial communities of adults. But, what about infants? An infant’s gut microbiome can have lifelong implications for health and disease. The Human Microbiome Project has demonstrated that an adults’ gut bacteria are the result of formative experiences in infancy, such as breastfeeding.5
Breastmilk and the surrounding skin on the breast contain a rich pool of microbes by which the infant gut can be seeded. But the critical steps and timeline of infant gut colonization are poorly understood. A 12-month study on 107 breastfeeding mothers and their infants demonstrated that 27.7% of an infant’s gut microbes come from breastmilk, while 10.4% come from areolar skin.6 Certainly, this and future research emphasize the importance of breastfeeding for shaping the infant gut microbiome.
Depression, genetics, and the gut
Many microbiome studies have found associations between the human gut microbiome and psychiatric conditions, such as depression, bipolar disorder, and others. However, individual studies have produced conflicting results due to the complexity of biological factors (i.e., diet, medication, etc.).
A large-scale study of nearly 6000 Finnish people was led by Michael Inouye and Guillaume Méric at the Baker Heart and Diabetes Institute. They investigated the link between genetic variants, diet, health status, and the gut microbiome.7 Firstly, they found that two clades of bacteria, Morganella and Klebsiella, have a causal effect on major depressive disorder (MDD) in study participants. Secondly, changes in Morganella gut bacteria were also associated with a genetic variant in PDE1A. This genetic variant has been linked to depression and other psychiatric disorders. In conclusion, the study sheds light on the complex interplay between genetics, the environment, the gut microbiome, and human physiology.
The human gut microbiome…in space!
Technological advances have enabled humans to enter extreme environments, like space. While incredible, a trip to space is physiologically challenging for the normal Earth-bound human, as it involves, confinement in small spaces and exposure to microgravity and radiation. As a result, these reasons makes it for an interesting model environment by which to study the human microbiome.
Using a pair of identical twins, Garrett-Bakelman et al. compared the impact of a 1-year spaceflight on one twin’s gut microbiome, compared to the other who remained on Earth.8 The flight subject underwent more changes in the composition and function of the microbiome while in space than the twin that stayed on Earth. Microbiome-derived metabolites were also altered in the twin that traveled to space. While in-flight, the flight subject experienced an increase in the ratio of Firmicutes to Bacteroidetes (F/B) bacteria, which was not seen in the other twin. The F/B ratio returned to normal following return to Earth from spaceflight. The health implications of these changes aren’t fully understood yet. However, follow-up studies of humans in extreme environments will shed light on the effect of these changes on human physiology.
Out of the gut, into the root
With a steady increase in the human population, there is increasing pressure to improve the productivity of staple crops, such as rice, a major food source worldwide. The two major types of rice cultivated are indica and japonica and they differ significantly in their nitrogen use efficiency (NEU; defined as the ratio of crop nitrogen uptake to total input in the soil), with indica being more efficient. In part, this is due to natural variation in the nitrate transporter and sensor, NRT1.1B. However, the root microbiome may also play a role, as it can metabolize different organic and inorganic forms of nitrogen.9
Zhang et al. analyzed 68 indica and 27 japonica varieties and found distinct differences in the root microbiome, with indica-enriched bacteria that associated with the presence of the NRT1.1B gene.9 Using this data, the group generated an indica-enriched synthetic bacterial community. They found that inoculation of an indica variety with the bacterial mix, along with an organic nitrogen source, enhanced NEU and rice growth, compared to inoculation with a japonica-enriched community. In conclusion, an increased understanding of plant genetics, the root microbial community, and nutrient utilization can help rationally design bacterial communities that increase productivity and shape more sustainable agricultural practices.
Infographic: Unearthing the full magnitude of microbiome research
Microbes in seawater
Seawater is teeming with microbes with a single milliliter of seawater containing up to 10 million viruses and 1 million bacteria.10 In addition, humans in costal regions like to live, play, and eat, this microbial community has significant implications for human health: Enterococcus, Enterobacteriaceae, and other pathogens can cause illness in swimmers and beachgoers. Thus, understanding the microbes that are present in coastal environments and their various transmission routes from “sea to sand” is important for protecting those living there.
Sea spray aerosols (SSAs) transmit some microbes from the ocean to the land. The SSAs are generated from breaking waves on the coastline. These SSAs have been shown to contain microbes and a recent paper used NGS to characterize the microbial community found in SSAs on three sandy California beaches.11 On average, there were about 6,100 bacterial cells/m3 in SSAs and clinically-relevant pathogens. Some of them are Staphylococcus epidermidis and Rothia mucilaginosa. Thus, the SSAs microbiome could be an important factor in protecting human health in coastal environments.
Continuing the expansion of microbiome research
As sequencing continues to get cheaper, automation more widespread, and extraction reagents less biased, our understanding of the microbiomes on (and off) Earth will continue to grow. Thermo Fisher Scientific offers a wide range of solutions for all scales of microbiome applications and research areas.
With MagMAX Microbiome Ultra Nucleic Acid Isolation Kits, you can extract DNA and RNA from microbial communities in several different sample types. Nucleic acid extraction can also be automated and scaled using our KingFisher Sample Purification Instruments, reducing hands-on time and providing high-quality, NGS-ready DNA or RNA. And we offer versatile NGS platforms for analyzing free-living or host-associated microbiomes.
For more on the microbiome check out:
- The Human Microbiome: New Frontiers in Medical Research
- MagMAX Microbiome Ultra Nucleic Acid Isolation
This article is for Research Use Only. Not for use in diagnostic procedures.
- Allaband C, McDonald D, Vázquez-Baeza Y, et al. Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. Clin Gastroenterol Hepatol. 2019;17(2):218-230. doi:10.1016/j.cgh.2018.09.017
- NIH Human Microbiome Project defines normal bacterial makeup of the body. NIH website: https://www.nih.gov/news-events/news-releases/nih-human-microbiome-project-defines-normal-bacterial-makeup-body. Accessed March 17, 2022. Published June 13, 2012.
- Huberman A. DR. JUSTIN SONNENBURG: HOW TO BUILD, MAINTAIN & REPAIR GUT HEALTH. Huberman Lab. 2022. Available at: https://hubermanlab.com/dr-justin-sonnenburg-how-to-build-maintain-and-repair-gut-health/. Accessed March 17, 2022.
- Thompson LR, Sanders JG, McDonald D, et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017;551(7681):457-463. doi:10.1038/nature24621
- Ding T, Schloss PD. Dynamics and associations of microbial community types across the human body. Nature. 2014;509(7500):357-360. doi:10.1038/nature13178
- Pannaraj PS, Li F, Cerini C, et al. Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome. JAMA Pediatr. 2017;171(7):647-654. doi:10.1001/jamapediatrics.2017.0378
- Qin Y, Havulinna AS, Liu Y, et al. Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort. Nat Genet. 2022;54(2):134-142. doi:10.1038/s41588-021-00991-z
- Garrett-Bakelman FE, Darshi M, Green SJ, et al. The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. Science. 2019;364(6436):eaau8650. doi:10.1126/science.aau8650
- Zhang J, Liu YX, Zhang N, et al. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nat Biotechnol. 2019;37(6):676-684. doi:10.1038/s41587-019-0104-4
- Wilhelm SW, Subtle CA. Viruses and Nutrient Cycles in the Sea: Viruses play critical roles in the structure and function of aquatic food webs. Bioscience. 1999;49(10):781-788. https://doi.org/10.2307/1313569
- Graham KE, Prussin II AJ, Marr LC, Sassoubre LM, Boehm AB. Microbial community structure of sea spray aerosols at three California beaches. FEMS Microbiol Ecol. 2018;94(3):fiy005. https://doi.org/10.1093/femsec/fiy005
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