100 for 100: Bioinformatics at ATCC

Item 35/100: The Mosquito Killer
Scott Nguyen, PhD, Senior Biocuration Scientist
ATCC® 35646™ – Bacillus thuringiensis Berliner

It’s May and summer is just peeking around the corner. Summer conjures the great outdoors with barbeques, gardening, vacations—and mosquitoes. Fortunately, the biocontrol agent Bacillus thuringiensis var. israelensis (Bti) has been studied and used for its potent effects on mosquito larva.¹ Bti-based products, such as Mosquito Dunks or Mosquito Bits, are used to control mosquitoes and other related pests of the Diptera order. Bti is an excellent biocontrol agent as it is lethal against mosquitoes while nontoxic to humans, mammals, fish, and beneficial insects like honeybees.² As a natural product, it has been used extensively for at least 35 years with no decreased susceptibility in target pests, making it one of the best environmentally friendly biocontrol agents.³

B. thuringiensis (ATCC® 35646™) is a delta endotoxin–producing strain that was isolated in the 1970s from a raw sewage pond in Israel and was later whole-genome sequenced at ATCC. The heat stable toxin from this strain was noted to have strong larvicidal activity against mosquito pests.⁴ As mosquitoes can carry important human pathogens like Plasmodium falciparum, Zika virus, and West Nile Virus, B. thuringiensis strains like ATCC® 35646™ and its engineered derivatives will play an important role in human health.⁵

Item 36/100: Bee-yond the Hive – How Gilliamella apicola Keeps Honeybees Humming
Nikhita Puthuveetil, MS, Senior Bioinformatician
ATCC® BAA-2448™ – Gilliamella apicola Kwong and Moran

Darting from budding flowers, their bodies tinged with a powdery yellow hue, honeybees work hard to collect nectar and pollen for their hive. However, these food sources can contain toxic sugars that can reduce the life span of adult bees.⁶ To digest these sugars, honeybees require the help of Gilliamella apicola, a gram-negative bacterial species found in the honeybee and bumblebee gut microbiome.⁷ Compared to that of other insects, the gut microbiome of the honeybee is quite simple and consistent across bees; G. apicola is one of the predominant saccharolytic fermenters in the bee gut microbiome, with all worker honeybees acquiring it by adulthood.⁸ The bacteria can metabolize many different sugars, including toxic sugars like mannose, xylose, and rhamnose,⁹ allowing bees to survive on a variety of nectars and pollens. In addition, G. apicola plays another role in protecting the honeybee by forming biofilms to defend against pathogens.¹⁰ Be it pesticides, dwindling food sources, pathogens, or toxic sugars, honeybees face numerous challenges as they make their way collecting pollen flower by flower. A small but mighty ally, G. apicola plays a monumental role in the health and survival of bees, ensuring they can keep buzzing about.

Item 37/100: A Shucking Danger for Oyster Lovers with Hemochromatosis
Ana Fernandes, BS, Supervisor, Laboratory Operations
ATCC® 27562™ – Vibrio vulnificus (Reichelt et al.) Farmer emend. West et al.

It’s a summer day in the Chesapeake Bay, and you’re enjoying a fresh oyster on the half-shell. However, this seemingly delightful experience could harbor a hidden danger—one that could be fatal if you have a certain genetic condition. Vibrio vulnificus, a gram-negative, halophilic bacillus commonly found in warm, brackish coastal waters was first isolated by the Centers for Disease Control and Prevention in the United States in 1964 and the strain ATCC® 27562™ was received and accessioned at ATCC in 1972. This organism has a dangerous affinity for undercooked seafood, especially raw oysters, and is responsible for over 95% of seafood related deaths in the United States.¹¹

While this organism can pose a threat to anyone who indulges in the delicacy, it presents a particular dangerous risk for individuals with hemochromatosis. Hemochromatosis is a genetic condition that causes the body to excessively absorb and store iron. This iron-rich environment is the perfect breeding ground for V. vulnificus to thrive and result in severe, fast-moving conditions that can lead to wound infection, amputation, organ failure and even death. In fact, the mortality rate for hemochromatosis patients who contract a V. vulnificus infection can be as high as 50% and males over the age of forty are at a greater risk.¹² Given the serious health risks posed by V. vulnificus for individuals with hemochromatosis, it is important to educate the public and increase awareness about the dangers of consuming raw or undercooked seafood. Currently, the ATCC Genome Portal has fourteen published genomes of this species with more genomes being added each quarter, underscoring the ongoing research efforts to better understand this deadly pathogen.

Item 38/100: Nature's Pharmacy: Actinomadura fibrosa
John Bagnoli, BS, Bioinformatics Senior Manager
ATCC® 49459™ – Actinomadura fibrosa Mertz and Yao

Actinomadura produces diverse bioactive metabolites with significant pharmaceutical potential. Initially mistaken for a fungus due to its filamentous structure, it was later identified as an aerobic actinomycete. Actinomadura, including the fibrosa species, is known to produce over 200 secondary metabolites, with polyketides, nonribosomal peptides, and hybrid polyketide-nonribosomal peptides being the most prominent.¹³

Polyketides and hybrid polyketide-nonribosomal peptides are compounds used in the treatment of various cancers. Examples include antibiotics like anthracyclines and angucyclines, known for their potent antitumor properties and widely used in chemotherapy to treat cancers such as leukemia and breast cancer. Additionally, these compounds are used to produce matlystatins, which serve as inhibitors of matrix metalloproteinases (MMPs). MMPs are enzymes involved in tissue remodeling and have been implicated in diseases like cancer and arthritis.

Nonribosomal peptides produce compounds such as madurastatins, which exhibit strong antimicrobial activities and show promise in combating antibiotic-resistant bacteria, making them valuable in the fight against superbugs.¹⁴ The metabolites produced by A. fibrosa and related species hold great promise for developing new antibiotics, anticancer agents, and other therapeutic drugs. As research continues, the pharmaceutical potential of these compounds is likely to expand, offering new hope for treating a wide range of diseases.

Item 39/100: An Apple a Day Won’t Keep the Fire Blight Away
Kaitlyn Gaffney, MS, Biologist, Sequencing & Bioinformatics
ATCC® 49946™ – Erwinia amylovora (Burrill) Winslow et al.

Erwinia amylovora was the first bacterium discovered to cause disease in plants during the 1800s and is considered one of the "top ten" bacteria in molecular plant pathology.¹⁵ It is responsible for causing the disease fire blight in species within the Rosaceae family, particularly apple and pear trees. Fire blight was first documented in New York State during the 18^th century but has since spread worldwide, causing significant economic and food production destruction.¹⁶

The bacterium invades plant tissue through small wounds or the hypanthium in flowers and then moves through the plant’s vascular tissue, eventually leading bacteria-laden fluid to ooze from cankers on the plant. This nectar-like fluid attracts insects which, in conjunction with wind and farming tools, leads to a rapid spread of E. amylovora. As the bacterium spreads through the plant, the tissue first appears water-soaked before wilting and darkening over several weeks, resulting in a burnt appearance—hence the name fire blight. If left untreated, E. amylovora can wipe out entire orchards.

Fire blight management is difficult due to a lack of systemic treatment and the concern of antibiotic resistance. Current control methods include pruning, tool sterilization, and chemical treatments. Pruning can be effective when the disease is contained to the flowers or shoots but infective once the spread reaches inside the xylem. Copper sprays and antibiotics, particularly streptomycin, are widely favored treatments.¹⁷ However, these treatments raise concern about amplifying the prevalence of streptomycin-resistant E. amylovora strains. There are also environmental concerns with the widespread use of antibiotic treatments leading to other bacteria species to becoming resistant. The complete genome of E. amylovora strain Ea273 (ATCC® 49946™) along with several other Erwinia species are available on the ATCC Genome Portal. These high quality, authenticated reference genomes could lead to novel insights into how to combat this harmful pathogen.

Item 40/100: Bat White-Nose Syndrome: An Emerging Fungal Pathogen
Briana Benton, BS, Program Manager, Sequencing & Bioinformatics
ATCC® MYA-4855™ – Pseudogymnoascus destructans (Blehert et Gargas) Minnis et Lindner

Pseudogymnoascus destructans is a psychrophilic fungus that was first isolated from a cave in New York during the winter of 2006-2007. Since then, it has spread across the United States and Canada. This fungal pathogen is responsible for causing White-Nose Syndrome (WNS), a fatal disease impacting hibernating bats across North America. The disease derives its name from the distinctive white fungal growth observed on the noses, ears, and wings of affected bats.

P. destructans thrives in dark, cool habitats and produces conidia (asexual spores) that are naturally dispersed into the environment.¹⁸ The spores then germinate upon contact with the skin of hibernating bats, leading to the formation of septate hyphae that invade and colonize the epidermal tissues and alter physiological processes like circulation, body temperature, and metabolism. Often, the infected bats are not able to recover and starve before winter ends. Since its emergence, White-Nose Syndrome has caused mortality rates exceeding 90% in certain bat colonies.¹⁹ Species such as the Little Brown Bat (Myotis lucifugus), Northern Long-Eared Bat (Myotis septentrionalis), and Tri-colored Bat (Perimyotis subflavus) have been particularly affected. Such a rapid and severe decline in bat populations throughout North America has significant ecological implications as bats play a unique and vital role in our ecosystem regarding natural insect control and pollination.²⁰

ATCC is committed to providing well-characterized isolates to the research community to facilitate a better understanding through research. Further research and development are needed to support healthy bat populations and develop potential treatments like antifungal agents and biological controls to decrease infection rates and improve bat survival rates.

Item 41/100: A Model Organism
Scott Nguyen, PhD, Senior Biocuration Scientist
ATCC® 39006™ – Prodigiosinella aquatilis Hugouvieux-Cotte-Pattat et al.

When Prodigiosinella aquatilis strain SC 11,482 (ATCC® 39006™) was deposited into the collection, ATCC biologists remarked on its unusualness. Due to its production of prodigiosin, a red pigment characteristic of Serratia marcescens, the strain was originally identified and then deposited into the ATCC collection as Serratia sp. Since then, a 2024 study by Hugouvieux-Cotte-Pattat et al. resulted in the reclassification of this strain as a member of a new genus of bacteria called Prodigiosinella, settling its decades-long misidentification.²¹

This strain has proven to be a useful model organism for studying the production of the carbapenem antibiotic 1-carbapenen-2-em-3-carboxylic acid, the production of gas vesicles for flotation, and the biosynthesis of prodigiosin.^22,23 Prodigiosin, a prodiginine, is being actively studied for its anticancer, antimalarial, and immunosuppressant properties.²⁴ You’ve likely seen this pigment before—the pink discolorations on tile grout, in bathtubs, and in toilets.²⁵ A dioxygenase gene from P. aquatilis was also recently studied for its ability to biotransform components of clove tree essential oils into vanillin, the primary component of vanilla bean extract.²⁶ To support these studies and to help provide more insights on this unusual bacterium, ATCC has whole-genome sequenced this strain and provided that data in the ATCC Genome Portal.

Item 42/100: Resilient Acidobacteria from the Arctic Tundra Biome
Suman Rawat, PhD, Lead Technical Writer
ATCC® BAA-1857™ – Granulicella mallensis Mannisto et al.

The soil microbiome plays a vital role in soil fertility as well as plant and human health. However, most soil microbiota remain uncharacterized and uncultured, with vast metabolic potential encoded in their genomes. Arctic environments harbor about one-third of the total global soil carbon pool, which is predicted to be impacted by climate change and microbial turnover. Acidobacteria, spanning 26 distinct phylogenetic subdivisions, represent one of the most ubiquitous and resilient bacterial phyla in diverse extreme environments. Acidobacteria grow very slowly, requiring several days to weeks to form visible colonies on complex, low-nutrient media.

Novel cold-adapted fastidious strains of Acidobacteria were isolated from the Arctic tundra using specialized growth techniques and then deposited in the ATCC repository. Biochemical and physiological analyses indicated that these novel species are active in nutrient-limiting and permafrost-like, low-temperature conditions in the Arctic tundra with the potential to form biofilms. Phylogenetic analysis showed that some of these isolates are novel type strains of the genus Granulicella in subdivision 1 of Acidobacteria.^27,28 Whole-genome sequencing of the Arctic isolates showed circular chromosomes ranging in size from approximately 4 to 6.0 Mbp with about 4000-5000 protein-coding genes and 50-55 RNA genes. In addition, the G. tundricola genome consists of five mega plasmids. Deeper insights into genome analysis revealed metabolic versatility with gene modules encoding for enzymes involved in the carbohydrate breakdown, utilization, biosynthesis, and transport of diverse structural exopolysaccharides.^29-31 Further, comparative genome analysis revealed functional activities encoded in biosynthetic gene clusters involved in the biogeochemical cycling of carbon and resilience to extreme cold and oligotrophic conditions in the Arctic tundra.³²

Did you know?

The ATCC Genome Portal initially started with only 250 bacterial genomes and now has 5,500 genomes from a diverse group of genera and various kingdoms.

References

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