Deep Functional Profiling of Wild Animal Microbiomes Reveals Probiotic Bacillus pumilus Strains with a Common Biosynthetic Fingerprint

Baranova, M.N.; Kudzhaev, A.M.; Mokrushina, Y.A.; Babenko, V.V.; Kornienko, M.A.; Malakhova, M.V.; Yudin, V.G.; Rubtsova, M.P.; Zalevsky, A.; Belozerova, O.A.; Kovalchuk, S.; Zhuravlev, Y.N.; Ilina, E.N.; Gabibov, A.G.; Smirnov, I.V.; Terekhov, S.S.

Авторы: Baranova Margarita N., Kudzhaev Arsen M., Mokrushina Yuliana A., Babenko Vladislav V., Kornienko Maria A., Malakhova Maja V., Yudin Victor G., Rubtsova Maria P., Zalevsky Arthur, Belozerova Olga A., Kovalchuk Sergey, Zhuravlev Yuriy N., Ilina Elena N., Gabibov Alexander G., Smirnov Ivan V., Terekhov Stanislav S.
Журнал: International Journal of Molecular Sciences
Том: 23
Номер: 3
Год издания: 2022
Издательство: MDPI
Местоположение издательства: Basel, Switzerland
Номер статьи: 1168
DOI: 10.3390/ijms23031168
Аннотация: The biodiversity of microorganisms is maintained by intricate nets of interactions between competing species. Impaired functionality of human microbiomes correlates with their reduced biodiversity originating from aseptic environmental conditions and antibiotic use. Microbiomes of wild animals are free of these selective pressures. Microbiota provides a protecting shield from invasion by pathogens in the wild, outcompeting their growth in specific ecological niches. We applied ultrahigh-throughput microfluidic technologies for functional profiling of microbiomes of wild animals, including the skin beetle, Siberian lynx, common raccoon dog, and East Siberian brown bear. Single-cell screening of the most efficient killers of the common human pathogen Staphylococcus aureus resulted in repeated isolation of Bacillus pumilus strains. While isolated strains had different phenotypes, all of them displayed a similar set of biosynthetic gene clusters (BGCs) encoding antibiotic amicoumacin, siderophore bacillibactin, and putative analogs of antimicrobials including bacilysin, surfactin, desferrioxamine, and class IId cyclical bacteriocin. Amicoumacin A (Ami) was identified as a major antibacterial metabolite of these strains mediating their antagonistic activity. Genome mining indicates that Ami BGCs with this architecture subdivide into three distinct families, characteristic of the B. pumilus, B. subtilis, and Paenibacillus species. While Ami itself displays mediocre activity against the majority of Gram-negative bacteria, isolated B. pumilus strains efficiently inhibit the growth of both Gram-positive S. aureus and Gram-negative E. coli in coculture. We believe that the expanded antagonistic activity spectrum of Ami-producing B. pumilus can be attributed to the metabolomic profile predetermined by their biosynthetic fingerprint. Ultrahigh-throughput isolation of natural probiotic strains from wild animal microbiomes, as well as their metabolic reprogramming, opens up a new avenue for pathogen control and microbiome remodeling in the food industry, agriculture, and healthcare.
Добавил в систему: Рубцова Мария Петровна

	ИСТИНА	Войти в систему Регистрация
	ИСТИНА ЦЭМИ РАН
	Главная Поиск Статистика О проекте Помощь

ИСТИНА

ИСТИНА ЦЭМИ РАН

Deep Functional Profiling of Wild Animal Microbiomes Reveals Probiotic Bacillus pumilus Strains with a Common Biosynthetic Fingerprintстатья Исследовательская статья

Прикрепленные файлы