Sample data collection
The study was approved by the “Secretaría de Medio Ambiente y Recursos Naturales (SEMARNAT)” in Mexico under the collecting permit SGPA/DGVS/007736/20, and samples were collected following the Official Mexican Standard NOM-126-ECOL-2000 as a guideline to handle the reptiles.
Fieldwork was conducted in the La Malinche National Park (central Mexico), a high-mountain ecosystem that rises to 4461 m above sea level (m a.s.l.). Only adult males were considered in this study to avoid sex-dependent variation in lizard microbial communities (snout–vent length > 44.1 mm; Jiménez-Cruz et al., 2005). A total of 10 fecal samples and 10 cloacal samples were collected from ten individuals (two samples per individual) living at ~ 2600 m a.s.l. (19°13'39.5"N, 97°54'44.1"W). Once captured, lizards were transported in cloth bags to La Malinche Scientific Station at 3100 m a.s.l., housed separately in plastic boxes (20 × 30 × 15 cm), and the next day, each individual was exposed to sunlight to induce their natural defecation. Fecal samples were immediately collected upon defecation using sterile tweezers and transferred into sterile 1.5 mL tubes. Collection time did not vary among individuals. Thereafter, the exterior of the cloaca was cleaned with alcohol to prevent contamination from exogenous microbes. Cloacal samples were obtained using sterile rayon swabs with a diameter of 1 mm (COPAN, Italy), inserted in the cloacal opening, gently rotated, and transferred to sterile 1.5 mL tubes. Due to S. grammicus being a small lizard, the swab size was appropriately adjusted to its size, trying to retrieve mostly luminal microbiota rather than host DNA from cloacal epithelium. In addition, to ensure less contamination of cloacal swabs with feces, we tried to insert swabs ~ 10 mm into the cloaca and did not reach the rectal section, avoiding collecting any residual material after defecation. Fecal and cloacal samples were transported to the laboratory at 4°C in a cooler and stored at -20°C until DNA extraction.
DNA extraction and shotgun metagenomic sequencing
To obtain high-quality DNA that met the required standards for shotgun sequencing, the following extraction process was used: fecal samples were washed twice with 1 mL of 0.15 M decahydrated tetrasodium pyrophosphate, followed by two washes with 0.15 M phosphate buffer (pH 8). Cell lysis was achieved using thermo/mechanical disruption. DNA from cloacal swabs was also extracted using thermo/mechanical disruption for cell lysis, followed by precipitation with cold isopropyl alcohol and glycogen (see Supporting Information; Hernández et al., 2023). The extracted DNA was sequenced at the Roy J. Carver Biotechnology Center, University of Illinois (Champaign, IL, USA). Shotgun genomic libraries were constructed from 300 ng of DNA after sonication with a Covaris ME220 (Covaris, MA) to an average fragment size of 400 bp with the Hyper Library construction kit from Kapa Biosystems (Roche, CA). Libraries were electrophoresed on a 2% agarose gel. The size-selected libraries were amplified with 3 cycles of PCR and run on a Fragment Analyzer (AATI, Ankeny, IA) to confirm the absence of free primers and adaptor dimers, as well as the presence of DNA of the expected size range. Libraries were pooled in equimolar concentration and quantitated by qPCR on a Bio-Rad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA). The pooled shotgun libraries were sequenced on an Illumina NovaSeq 6000 SP lane with 2x150 nt paired-end configuration. Lastly, fastq read files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).
Bioinformatic analysis
Raw metagenomic reads were processed following the bioinformatic workflow developed for the 3D’omics European Union Horizon 2020 Project (https://3domics.eu/), available online as a Snakemake pipeline (Köster & Rahmann, 2012) at GitHub (https://github.com/3d-omics/mg_assembly), and based on the Earth Hologenome Initiative (https://www.earthhologenome.org/; see Leonard et al., 2024). Briefly, Fastp v.0.23.4 was used to remove adapters, and low-quality and short reads (Chen et al., 2018), and prokaryotic sequencing fractions were estimated using SingleM microbial fraction (Eisenhofer et al., prepint). Next, host-derived reads were removed by mapping against a reference host genome using Bowtie2 v.2.5.1 (Langmead & Salzberg, 2012) and Samtools v.1.18 (Danecek et al., 2021). We used the reference genome of the phylogenetically related species S. undulatus (NCBI accession number PRJNA656311; Westfall et al., 2021), due to the absence of a reference genome for S. grammicus. The unmapped metagenomic reads were assembled (samples were treated individually) and co-assembled (samples were pooled and processed together) into contigs by MEGAHIT v.1.2.9 (Li et al., 2016), and reads were mapped to all the contigs of the corresponding sample using Bowtie2 with default settings. Contigs were then binned using CONCOCT v.1.1 (Alneberg et al., 2014), MetaBAT2 v.1.7 (Kang et al., 2015) and MaxBin2 v.2.2.4 (Wu et al., 2016). Bins were polished with MAGScoT v.1.0.0 (Rühlemann et al., 2022) and their quality was assessed using CheckM2 (Chklovski et al., 2023). MAGs were dereplicated at 98% average nucleotide identity (ANI) using dRep v.3.4.3 (Olm et al., 2017). CoverM v.0.6.1 was used to calculate the percentage of reads mapping to each MAG (https://github.com/wwood/CoverM).
Dereplicated MAGs were taxonomically annotated using GTDB-Tk v.2.3.2 against the Genome Taxonomy Database (release 214) (Chaumeil et al., 2019; Parks et al., 2022). The phylogenetic tree of the MAGs was generated leveraging the phylogenetic placement of the previous step, by pruning the reference GTDB-tk genomes using the function keep.tip in ape v.5.7-1 (Paradis et al., 2004). Functional prediction of the MAGs was performed with DRAM v.1.4.6 (Shaffer et al., 2020) against the Pfam, KEGG, UniProt, CAZY, and MEROPS databases. We employed distillR (available at https://github.com/anttonalberdi/distillR) to distill functional annotations into Genome-Inferred Functional Traits (GIFTs), which serve as quantitative indicators of the capacity of each MAG to either degrade or produce key biomolecules. The reference database, comprising 328 metabolic pathways and modules from KEGG (Kanehisa et al., 2017) and Metacyc (Karp et al., 2002) databases, facilitated the conversion of raw annotations into 190 GIFTs.
Statistical analyses
Alpha diversities
All statistical analyses were performed using the R software v.4.3.2 (R Core Team, 2023). We determined neutral, phylogenetic and functional diversities of microbial communities using Hill numbers (Hill, 1973). Neutral Hill numbers represent species diversity without considering the degree of relatedness among MAGs, while phylogenetic Hill numbers incorporate branch-length information of the phylogenetic tree of the MAGs and functional Hill numbers consider functional differences among MAGs. Hill numbers differ by the parameter q, which determines the sensitivity of the measure to the relative abundance (Chao et al., 2014). For capturing effects of different components (neutral, phylogenetic and functional) and orders of diversity (q = 0 only accounts for presence/absence, and q = 1 weighs MAGs according to their relative abundances), species richness of q = 0, neutral diversity of q = 1, phylogenetic diversity of q = 1 and functional diversity of q = 1 were computed using Hilldiv2 v.2.0.2 (Alberdi & Gilbert, 2019). Linear mixed models were used to quantify differences in bacterial alpha diversity between sampling methods, with lizard ID included as random effect, using the function lmer from the lme4 package v.1.1–35.1 (Bates et al., 2015).
Beta diversities
The dissimilarities between fecal and cloacal MAGs composition were calculated in terms of Hill numbers by computing the Sørensen-type turnover from neutral, phylogenetic and functional beta diversities at order q = 1, using the hillpair function in Hilldiv2. Nonmetric multidimensional scaling (NMDS) ordination plots based on derived distance matrices were performed to visualise microbial composition variation. The betadisper function in vegan v.2.6-4 (Oksanen et al., 2023) was applied to test differences in dispersion within sampling methods. PERMANOVA was performed to test for differences in microbial composition between sampling methods using the adonis2 function in vegan, with individual identity as a blocking factor to control for repeated sampling using the strata function. To visualize bacteria according to their functional features, the MAGs were ordinated based on their GIFTs through a t-SNE analysis using the Rtsne package v.0.17 (Krijthe et al., 2017).
Differential taxonomic and functional abundances
Differential abundance analyses were performed to investigate which microbial taxa significantly differ between sampling methods, using ANCOM-BC2 package v.2.4.0 (Lin & Das Peddada, 2020). Considering the lizard ID random effect, differential abundance analyses were conducted at the MAG level, with log-fold changes between sample types and -log(p-values) visualized in a volcano plot, and at the phylum level, with results visualized in a bar chart. In addition, we calculated community-weighted values of GIFTs before comparing values between sample types using linear mixed models including lizard ID as random effect: (e.g. lmer(GIFT ~ sampletype + (1 | individual), data = ., REML = FALSE)). The resulting p-values were adjusted using the Bonferroni method to account for multiple testing.