Metagenomic Thermometer

Masaomi Kurokawa, Koichi Higashi, Keisuke Yoshida, Tomohiko Sato, Shigenori Maruyama, Hiroshi Mori, and Ken Kurokawa

DNA Research (2023) 30, dsad024 DOI:10.1093/dnares/dsad024

Press release (In Japanese only)

Researchers at National Institute of Genetics have developed a groundbreaking tool, the “Metagenomic Thermometer,” which predicts environmental temperatures by analyzing the DNA of microorganisms in any given habitat. This innovative approach offers new insights into how environmental conditions influence life at a microbial level and could have wide-reaching implications in environmental science, biotechnology, and human health.

In a trailblazing study published in DNA Research, a team led by Professor Ken Kurokawa has unveiled the “Metagenomic Thermometer.” This tool marks a significant leap in environmental microbiology, enabling scientists to gauge the temperature of an environment by studying the genetic makeup of its microbial inhabitants.

The “Metagenomic Thermometer” operates on a groundbreaking principle: Professor Kurokawa’s team have extended the concept of estimating the optimal growth temperature (OGT) of a microorganism from the amino acid frequency of its genetic information, and developed a method of estimating the ambient temperature from the amino acid frequency in the collective genetic information of the microbial community present.

This revolutionary method was rigorously tested across diverse ecosystems, including hot springs, soil samples, and even the human gut. Remarkably, when applied to human gut metagenomic samples, the thermometer could accurately estimate human body temperature, underscoring the profound interplay between our internal environment and the microbial world.

Professor Kurokawa’s team believes that this tool doesn’t just measure temperature — it offers a new lens to understand how temperature drives the assembly of microbial communities. By focusing on amino acid composition rather than just microbial species, the Metagenomic Thermometer provides a more nuanced view of how life adapts to its environment.

The implications of this research are vast. From monitoring climate change impacts on microbial biodiversity to optimizing conditions for biotechnological applications, and even understanding human health in relation to our microbiome, the Metagenomic Thermometer stands as a testament to the power of innovative scientific inquiry.

“This research not only presents a novel tool but also opens up new avenues for understanding the intricate relationship between life and the environment,” said Professor Kurokawa. “We are excited about the potential applications of the Metagenomic Thermometer in various fields, including ecology, medicine, and biotechnology.”

• Variation in Gut Microbiome with Body Temperature:
  The research proposes that body temperature significantly influences the gut microbiome composition. This revelation provides a deeper understanding of how bodily changes can impact gut health.
• Predicting Deep Body Temperature:
  Utilizing metagenomic analysis, the team has developed a ‘Metagenomic Thermometer’, which potentially allows for the estimation of human deep body temperature based on gut microbiota. This innovative approach offers a non-invasive method to gauge internal body temperature, a crucial health parameter.
• Personalizing Medical Treatments:
  The findings suggest exciting possibilities in tailoring treatments such as FMT and LBPs based on individual body temperatures. This could lead to more effective and personalized therapies for patients.
• Probiotics Tailored to Body Temperature:
  The research opens avenues for developing probiotics like yogurt and lactobacillus beverages specifically designed for individuals with varying body temperatures, enhancing their effectiveness.
• Future Research Directions:
  The team anticipates further exploration into how aging and diseases that lower body temperature affect gut microbiome composition. Additionally, the study’s methodologies could enhance predictions about bacterial community changes due to global warming, potentially influencing CO2 emission patterns.

For more information about this research, contact Office for Research Development.

– The study, “Metagenomic Thermometer,” was published in DNA Research.
– Interviews with the research team can be arranged upon request.
– High-resolution images and graphics explaining the Metagenomic Thermometer are available.

Contact:
Office for Research Development
National Institute of Genetics

National Institute of Genetics is a world-leading institution in genetics, genomics and bioinformatics. Our commitment to innovation and excellence places us at the forefront of global scientific endeavors.

• VITCOMIC2 and LEA are the basis of this research.
• “Metagenomic Thermometer” is here.

Miyagishima Group / Symbiosis and Cell Evolution Laboratory

Taming the perils of photosynthesis by eukaryotes: constraints on endosymbiotic evolution in aquatic ecosystems

Shin-ya Miyagishima

Communications Biology (2023) 6, 1150 DOI:10.1038/s42003-023-05544-0

An ancestral eukaryote acquired photosynthesis by genetically integrating a cyanobacterial endosymbiont as the chloroplast. The chloroplast was then further integrated into many other eukaryotic lineages through secondary endosymbiotic events of unicellular eukaryotic algae. While photosynthesis enables autotrophy, it also generates reactive oxygen species that can cause oxidative stress. To mitigate the stress, photosynthetic eukaryotes employ various mechanisms, including regulating chloroplast light absorption and repairing or removing damaged chloroplasts by sensing light and photosynthetic status. Recent studies have shown that, besides algae and plants with innate chloroplasts, several lineages of numerous unicellular eukaryotes engage in acquired phototrophy by hosting algal endosymbionts or by transiently utilizing chloroplasts sequestrated from algal prey in aquatic ecosystems. In addition, it has become evident that unicellular organisms engaged in acquired phototrophy, as well as those that feed on algae, have also developed mechanisms to cope with photosynthetic oxidative stress. These mechanisms are limited but similar to those employed by algae and plants. Thus, there appear to be constraints on the evolution of those mechanisms, which likely began by incorporating photosynthetic cells before the establishment of chloroplasts by extending preexisting mechanisms to cope with oxidative stress originating from mitochondrial respiration and acquiring new mechanisms.

Figure: Examples of unicellular organisms with primary chloroplasts originating from cyanobacterial endosymbiosis, secondary chloroplasts from eukaryotic algal endosymbiosis, and organisms exhibiting phagotrophy, phototrophy, and kleptoplasty. Figure courtesy of Dr. Onuma (Kobe Univ.) and Mr. Okada (Nat. Inst. of Genet.).

Nakamura Group / Genome Informatics Laboratory

A Practical Assembly Guideline for Genomes with Various Levels of Heterozygosity

Takako Mochizuki, Mika Sakamoto, Yasuhiro Tanizawa, Takuro Nakayama, Goro Tanifuji, Ryoma Kamikawa, Yasukazu Nakamura*
*Corresponding Author

Briefings in Bioinformatics (2023) 24, bbad337 DOI:10.1093/bib/bbad337

The advancement of long-read sequencing technologies, exemplified by subreads of Pacific Biosciences, has significantly advanced our ability to reconstruct genome sequences. While these technologies can generate long reads, they are plagued by high sequence errors. To address these errors and strive to construct long, highly accurate contig sets, various de novo assemblers have been developed.

In de novo assembly of diploid genomes, the complexity increases with higher heterozygosity. Therefore, heterozygosity is a significant factor influencing the completeness of de novo assembly. However, systematic evaluations of de novo assemblers for diploid genomes with various heterozygosity levels have not been conducted.

In this study, using genomes with varying levels of heterozygosity, we conducted a series of processes, including estimation of genome characteristics such as genome size and heterozygosity, de novo assembly, polishing, and removing contigs including alleles. We have presented a guideline for constructing a representative haplotype set based on heterozygosity levels.

This work was supported by JSPS grant-in-aid for Scientific Research on Innovative Areas, Platform for Advanced Genome Science [16H06279], and KAKENHI [15H05606 and 19H03274, 20H03305, 17H03723].

Computations were partially performed on the National Institute of Genetics supercomputer.

Figure: An evaluation process for genome assembly using genomes with various levels of heterozygosity

Kitano Group / Ecological Genetics Laboratory

First record of Macrobrachium mammillodactylus (Thallwitz, 1891) (Crustacea, Decapoda, Palaemonidae) from Japan.

Yusuke Fuke, Tomoaki Maruyama.

Check List (2023) 19, 821-826 DOI:10.15560/19.6.821

The freshwater prawn genus Macrobrachium has more than 270 known species, with remarkably high species diversity in tropical freshwaters. Most of the widely distributed species in the Pacific have amphidromous migratory life history, which allows them to expand their range via ocean currents.

In this study, Yusuke Fuke, JSPS Postdoctoral Fellow at the National Institute of Genetics, and Tomoaki Maruyama of Trend Design Co., Ltd. identified the specimens collected from Miyako Island as Macrobrachium mammillodactylus (Thallwitz, 1891) based on genetic and morphological analysis. This marks the first record of this species in Japan and its northernmost distribution. This species has been previously reported from Australia to central Taiwan. The specimens collected in this study were adults, suggesting that they likely overwintered on the island, indicating an expansion of their range to the Ryukyu Archipelago.

Range expansion from Southeast Asia to the Ryukyu Archipelago and Honshu has been observed in other southern freshwater shrimp species. By accumulating fundamental range data, we may be able to identify and predict the factors contributing to the range expansion of amphidromous species.

Figure: Macrobrachium mammillodactylus collected from Miyako Island, Japan. Photo by T. Maruyama.