REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Magnetic beads coated with anti-CD14 antibodies	Miltenyi Biotech	Cat#130050201; RRID: AB_2665482
Bacterial and virus strains
LPS from Escherichia coli, 100 ng/ml, Ultrapure	Invivogen	Cat#0111:B4
Klebsiella pneumoniae	This study	ATCC43816
Biological samples
Rectal swab in Universal Transport Medium	Copan	Cat#349C
Heparin tubes	BD Bioscience	Cat#367874
Chemicals, peptides, and recombinant proteins
Ficoll-Paque PLUS	GE Healthcare Life science	Cat#17144002
Maxwell RSC Whole Blood DNA Kit	Promega	Cat#AS1520
Human Luminex multiplex assay	R&D Systems	Cat#LXSAHM-04
BioPlex 200	BioRad	Cat#X10010027401
AllPrep DNA/RNA/Protein mini kit	Qiagen	Cat#80004
KAPA RNA Hyperprep with RiboErase	Roche	Cat#08098131702
Deposited data
Transcriptional monocyte RNA data	GEO database	GEO database: GSE160329
Microbiome sequence data	European Nucleotide Archive	ENA: PRJEB42265
Software and algorithms
R	R Core Team 2014	Version 4.1.1
Python (Linux/UNIX)	Python	Version 2.7.12
Other
Cell-repellent surface 48-well plate	Greiner Bio-One	Cat#677970
MACS LS columns	Miltenyi Biotech	Cat#130-042-401
Magnetic separator for MACS	Miltenyi Biotech	Cat#130-091-051