Protocol for isolating single species of bacteria with swarming ability from human feces

Hao Li; Lilli Hong; Wendy Szymczak; Erika Orner; Arkadiy I Garber; Vaughn S Cooper; Weijie Chen; Arpan De; Jay X Tang; Sridhar Mani

doi:10.1016/j.xpro.2024.102961

Protocol for isolating single species of bacteria with swarming ability from human feces

STAR Protoc. 2024 Apr 2;5(2):102961. doi: 10.1016/j.xpro.2024.102961. Online ahead of print.

Authors

Hao Li¹, Lilli Hong¹, Wendy Szymczak², Erika Orner², Arkadiy I Garber³, Vaughn S Cooper⁴, Weijie Chen⁵, Arpan De¹, Jay X Tang⁶, Sridhar Mani⁷

Affiliations

¹ Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
² Montefiore Medical Center, Bronx, NY 10467, USA; Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
³ Middle Author Bioinformatics, LLC., Tempe, AZ 85282, USA.
⁴ Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA; Center for Evolutionary Biology and Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA; Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA.
⁵ Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Intelligent Medicine Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China.
⁶ Brown University, Physics Department, Providence, RI 02912, USA.
⁷ Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Electronic address: sridhar.mani@einsteinmed.edu.

Abstract

Understanding the specific movements of bacteria isolated from human feces can serve as a novel diagnostic and therapeutic tool for inflammatory bowel disease. Here, we present a protocol for a microbial swarming assay and to isolate the bacteria responsible for swarming activity. We describe steps for identifying bacteria using MALDI-TOF mass spectrometry and whole-genome sequencing. We then detail procedures for validating findings by observing the same swarming phenotype upon reperforming the swarming assay. For complete details on the use and execution of this protocol, please refer to De et al.¹.

Keywords: Health Sciences; Mass Spectrometry; Microbiology; Sequencing.