Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging

length not shorter than 150 bp and not longer than 350 bp; no ambiguous bases (Ns). Quality filter was not applied because fastq files were not available. Then, OTUs were obtained by clus- tering reads at 97% of similarity using the UPARSE pipeline [45]. iii) Odamaki: Data from Odamaki et al. [10] include 367 community-dwelling Japanese (0– 104 years old). 16S rRNA gene V3-V4 amplicons were sequenced using an Illumina MiSeq instrument (Illumina, Inc., San Diego, CA, USA) with a MiSeq v3 Reagent Kit. DNA sequences (fastq files) are available in DDBJ under accession number DRA004160. Paired-end sequencing reads were merged using usearch and filtered with usearch using the following criteria: read length not shorter than 150 bp; average quality score greater than 25. OTUs were obtained by clustering sequencing reads at 97% following the UPARSE pipeline [45]. iv) Kong: Data from Kong et al. [36] include 168 Chinese healthy subjects (24–102 years old) from Dujiangyan and Ya’an, Sichuan province. 16S rRNA gene V4-V5 amplicons were sequenced on an Illumina MiSeq sequencer (Illumina, Inc., San Diego, CA, USA) using a 2×250 bp paired protocol. DNA sequences (merged paired-end fastq files) are available on the Sequence Read Archive under the accession number SRP076167. Sequencing reads were fil- tered using mothur [46] according to the following criteria: read length not shorter than 150 bp and not longer than 400 bp; no ambiguous bases (Ns); no homopolymers longer than 8 bp, average quality score greater than 25. OTUs were obtained by clustering sequencing reads at

97% following the UPARSE pipeline [45]. v) Biagi: Data from Biagi et al. [20] include 69 Italian healthy subjects (22–109 years old) from Emilia-Romagna. 16S rRNA gene V3-V4 amplicons were sequenced on an Illumina MiSeq sequencer (Illumina, Inc., San Diego, CA, USA) using a 2×300 bp paired end protocol. DNA sequences (fasta files) are available on MG-RAST under the project id 17761. Since spe- cific filters and parameters applied for the pre-processing of the reads are not detailed in the original paper, we used the filters of the Kong data set, adapting the parameters to the different read length. Hence, sequencing reads were filtered using mothur [46] according to the follow- ing criteria: read length not shorter than 400 bp and not longer than 500 bp; no ambiguous bases (Ns); no homopolymers longer than 8 bp. Quality filter was not applied because fastq files were not available. OTUs were obtained by clustering sequencing reads at 97% following the UPARSE pipeline [45]. vi) Bian: Data from Bian et al. [37] include 1125 Chinese healthy subjects (3–109 years old) self-reported as having a personal and family history of extreme health. Among these 212 are young soldiers (19–24) who passed the standard military entrance medical examination, and whose grandparents lived to be at least 85 years. 16S rRNA gene V4 amplicons were sequenced on an Illumina MiSeq sequencer (Illumina, Inc., San Diego, CA, USA) using a 2×300 bp paired end protocol. OTUs across all samples were obtained from the Supplementary Information of the original paper.

Modeling of the Relative Species Abundance distribution (RSA) According to Volkov’s model [31], the population dynamics of all species included in the eco- system is a birth-death process with a further constant influx. The dynamics is hence ruled by three parameters: a birth rate (b), a death rate (d) and an immigration term (S) that represents a density dependent constant influx of individuals into the population, and can be expressed by the deterministic equation dn dt ¼ b � n d � n þ S ð7Þ PLOS ONE Gut microbiota biodiversity and healthy aging PLOS ONE | https://doi.org/10.1371/journal.pone.0237207 October 30, 2020 14 / 23