REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
F. prausnitzii Fp1	This paper	N/A
F. prausnitzii Fp4	This paper	N/A
F. prausnitzii Fp14	This paper	N/A
F. prausnitzii Fp28	This paper	N/A
F. prausnitzii Fp40	This paper	N/A
F. prausnitzii Fp45	This paper	N/A
F. prausnitzii Fp77	This paper	N/A
F. prausnitzii Fp137	This paper	N/A
F. prausnitzii Fp360	This paper	N/A
F. prausnitzii Fp944	This paper	N/A
F. prausnitzii Fp1043	This paper	N/A
F. prausnitzii Fp1160	This paper	N/A
Biological samples
Healthy, MCI, and AD fecal samples	This paper	N/A
Chemicals, peptides, and recombinant proteins
Nextera Index Kit	Ilumina	FC-131-1002
TruSeq Nano DNA Library Prep Kit	Ilumina	FC-121-4003
Deposited data
16S rRNA sequencing (Japanese, n = 43)	This paper	NCBI Sequence Read Archive: PRJNA679347
Whole-genome sequencing (12 isolates of F. prausnitzii)	This paper	NCBI Genome: PRJNA679348
Whole-metagenome shotgun sequencing (Japanese, n = 43)	This paper	NCBI Sequence Read Archive: PRJNA679346
RNA sequencing of mouse hippocampus (n = 51)	This paper	NCBI Sequence Read Archive: PRJNA735905
Genome of F.prausnitzii A2-165	GenBank	GCA_010509575.1
Genome of F.prausnitzii S3L/3	GenBank	GCA_000209855.1
Genome of F.prausnitzii L2-6	GenBank	GCA_000210735.1
Experimental models: Organisms/strains
ddY mice	Japan SLC, Inc.	RRID: MGI:5558113
Software and Algorithms
QIIME2	Bolyen et al.45	https://qiime2.org/
MEGA	Kumar et al., 201846	https://www.megasoftware.net/
Circlator	Hunt et al.47	http://sanger-pathogens.github.io/circlator/
CheckM	Parks et al.48	http://ecogenomics.github.io/CheckM/
Prokka	Seemann49	https://vicbioinformatics.com/software.prokka.shtml
InterProScan	Jones et al.50	http://www.ebi.ac.uk/interpro/search/sequence/
TMHMM	Krogh et al.51	http://www.cbs.dtu.dk/services/TMHMM/
Roary	Page et al.52	https://sanger-pathogens.github.io/Roary/
Orthofinder	Emms and Kelly53	https://github.com/davidemms/OrthoFinder
DIAMOND	Buchfink et al.54	https://github.com/bbuchfink/diamond
Cutadapt	Martin55	https://cutadapt.readthedocs.io/en/stable/
Bowtie2	Langmead and Salzberg56	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Kallisto	Bray et al.57	https://pachterlab.github.io/kallisto/about
Hisat2	Kim et al.58	https://daehwankimlab.github.io/hisat2/
StringTie	Pertea et al.59	http://ccb.jhu.edu/software/stringtie/
SAMtools	Li et al.60	http://samtools.sourceforge.net/