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Genome sequencingWe sequenced the genomes of 35 strains of B. pseudocatenulatum (Supplementary Table S1). These strains were isolated at the Yakult Central Institute and the species were identified based on the 16S rRNA gene sequence analysis. These strains have been isolated in the course of various studies over the past few decades, including many studies on infants and adults. B. pseudocatenulatum cultures were anaerobically incubated in modified Gifu anaerobic medium (Nissui Pharmaceutical, Tokyo, Japan) supplemented with lactose and glucose (both 0.5% wt/vol) at 37 °C for 16 h. These culture conditions were applied throughout the study unless stated otherwise. The detailed procedures for genomic DNA extraction, library preparation for MiSeq (Illumina, San Diego, CA, USA), MinION (Oxford Nanopore Technologies, Oxford, UK) and PacBio RS2 (Pacific Biosciences, Menlo Park, CA, USA), and sequencing are described in the Supplementary Methods.Genome assembly, gene prediction and pangenome analysisWe used Unicycler [26] with default parameters for both short-read and hybrid assembly, and Prokka [27] with default parameters for annotating the reconstructed genomes and those downloaded from the RefSeq database. The annotated genomes were then processed with Roary [28] with a default gene identity cut-off parameter of 95% for species level pangenome analysis. A representative sequence from each gene cluster was translated into a protein sequence, and CAZymes were identified using the dbCAN2 server [29]. Proteins were considered CAZymes if they were identified using HMMER, DIAMOND and Hotpep with default parameters. We then built a CAZyme gene distribution matrix (Supplementary Table S2) based on the gene presence-absence table determined using Roary.Carbohydrate utilisation assaysStrains of B. pseudocatenulatum were cultured until they reached the exponential phase, centrifuged, and then, the resulting pellets were suspended to an OD600 of 0.2 in modified peptone yeast extract (PY) medium (100 mM PIPES, pH 6.7, 2 g/L peptone, 2 g/L BBL trypticase peptone, 2 g/L bacto-yeast extract, 8 mg/L CaCl2, 19.2 mg/L MgSO4 ∙ 7H2O, 80 mg/L NaCl, 4.9 mg/L hemin, 0.5 g/L L-cysteine hydrochloride and 100 ng/L vitamin K1). These suspension cultures were inoculated (1% vol/vol) into modified PY medium supplemented with 0.5% (wt/vol) XOS (Xylo-Oligo95P, B Food Science, Aichi, Japan) (PY-XOS), wheat arabinoxylan (Megazyme, Bray, Ireland) (PY-AX) or beechwood xylan (Sigma-Aldrich, Darmstadt, Germany) (PY-XY) and covered with sterile mineral oil (50 μL) to prevent evaporation. Growth was monitored anaerobically by measuring the OD600 using a PowerWave 340 plate reader (BioTek, Winooski, VT, USA) every 30 min in an anaerobic chamber for 48 h. The organic acids produced in PY-XY were analysed using high-pressure liquid chromatography as described [8].Cloning, expression and purification of recombinant BpXyn10AThe GH10 domain of the BpXyn10A gene was amplified by PCR using the primers xynA-GH-F (5’-CATCATCATCATCATGCGGAAGGCGACGCCGTA-3’) and xynA-GH-R (5’-AGCAGAGATTACCTAATCCTTGAATGCGTTCATGC-3’), with the genomic DNA of YIT 11027 as a template. A linearised vector was synthesised by PCR using primers pColdII-F (5’-GTAATCTCTGCTTAAAAGCACAGAATCTA-3’) and pColdII-R (5’-ATGATGATGATGATGATGCACTTTGT-3’), and the pColdII vector (Takara Bio, Otsu, Japan) as a template. These fragments were ligated using In-Fusion HD Cloning Kits (Takara Bio, Otsu, Japan), resulting in pColdII-xynA. Escherichia coli BL21 was transformed with pColdII-xynA and cultured to express recombinant BpXyn10A as described by the manufacturer. Bacterial cells were harvested by centrifugation and lysed with B-PER Bacterial Cell Lysis Reagent (Thermo Fisher Scientific, Waltham, MA, USA) containing lysozyme at 100 µg/mL and 10 U/mL of DNase I. Recombinant BpXyn10A was further purified using Ni-NTA Spin Column (Qiagen, Hilden, Germany) and analysed by SDS-PAGE.Endo-xylanase activity assayB. pseudocatenulatum YIT 11027, YIT 11952 and YIT 4072T cells were grown anaerobically in PY-AX or PY-XOS medium for 16 h. Cultures (1.5 mL) were centrifuged (8000× g for 2 min at room temperature); then, supernatants were sterilised by passage through a 0.22-μm filter. Pelleted cells were washed with modified PY medium and resuspended in 1.5 mL of the same medium. The endo-xylanase activity of the supernatant and the cell fractions were assayed using Xylanase Assay kits (XylX6 method) (Megazyme, Bray, Ireland) as described by the manufacturer. According to the manufacturer, this kit is designed to specifically detect only endo-xylanase activity, and not xylosidase or exo-xylanase enzyme activity.Purified BpXyn10A-added cultureB. pseudocatenulatum YIT 4072T and Ba. ovatus YIT 6161T cells were cultured anaerobically until they reached the exponential phase. Thereafter, cultures (200 μL) were centrifuged (8000× g for 2 min at room temperature), then pelleted cells were resuspended in modified PY medium (500 μL), and inoculated (1% vol/vol) into PY-AX medium supplemented with 0, 10, 100 and 1000 ng/mL purified recombinant BpXyn10A. Growth was monitored anaerobically by measuring the OD600 using the PowerWave 340 plate reader.RNA-seq analysisB. pseudocatenulatum YIT 11952 was cultured in modified PY medium supplemented with 0.5% (wt/vol) lactose, xylose, XOS, beechwood xylan or arabinoxylan and harvested at mid- to late-log phase. The detailed procedures for total RNA extraction, rRNA removal and sequencing using MiSeq are described in the Supplementary Methods. We obtained a total of 23 million paired-end reads. Low-quality bases (average quality More

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