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PatientsStool samples from a total of 52 patients with varying stages of CKD were collected in this study: CKD3A (n = 12), CKD3B (n = 11), CKD4 (n = 15), CKD5 (n = 4) and ESRD (n = 10) (Table 1). Patients’ characteristics are summarized in Table 1. Among 52 patients, 31 were reported to have Type 2 diabetes mellitus and 7 patients were reported to have human immunodeficiency virus (HIV) infection. As expected, urine protein creatinine ratio, serum creatinine and blood urea nitrogen level increased with progressing stages of CKD (CKD 3A to ESRD). There was no significant difference in fat, protein, carbohydrates, dietary fiber and calorie intake between CKD patients with different stages (Supplementary Table S1).Table 1 Patients’ characteristics.Full size tableAlpha and beta-diversityRichness and Shannon index were not significantly different between different patient groups, meanwhile the CKD5 group showed a significant decrease in Simpson diversity compared with CKD 3A (FDR  More

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Sub-regionsThe study region focuses on 18 sub-regions within the Pacific mountain ranges of North American overlapping with the range of Pacific Salmon with >1.5% glacier cover (Figs. 1 and 2). The term “sub-region” here refers to either a single major salmon watershed or aggregates of small coastal watersheds, which range in area from ~13,000 to ~68,000 km2. For sub-regions within Alaska, USA, we accessed boundary data from the Watershed Boundary Database at the USGS (https://www.usgs.gov/). For sub-regions within British Columbia, Canada, we accessed boundary data from the Freshwater Atlas of British Columbia (https://catalogue.data.gov.bc.ca/). Pacific salmon range data were from the National Center for Ecological Analysis and Synthesis (Fig. 1). The study region covers ~623,000 km2 across British Columbia, Canada and Alaska, USA and ~20% of the total North American range of Pacific salmon.Glacier outlinesOutlines for the 45,963 glaciers within the study region were obtained from the Randolph Glacier Inventory v6.0 (https://www.glims.org/RGI/; RGI v6.0), which provides a globally complete data set of glacier outlines outside of Greenland and Antarctic ice sheets17. These glaciers cover a total area of ~81,000 km2, which corresponds to 80% of the total glacier area in the Pacific mountain ranges within North America. The glacier outlines refer roughly to the years 2009 ± 2 for Alaska, and 2004 ± 5 for Western Canada17,53. Glacierization for each of 18 sub-regions ranges from 1.5 to 52%.Present-day streamsSynthetic stream networks were constructed from Digital Elevation Models (DEMs) for each of the 18 sub-regions using Geographic Information Systems (GIS; ArcGIS 10.6 and QGIS 2.18) hydrology tools to represent present-day streams throughout the study region. Specifically, we used Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) global DEMs v2.0 with a spatial resolution of ~30 m54. Open access synthetic stream network datasets such as the National Hydrography Dataset (NHD) from the USGS and the Freshwater Atlas from the British Columbia government are available but were not used due to inconsistencies in spatial resolution across the study region. From our synthetic stream networks, we eliminated all stream segments that overlapped with the RGI glacier outlines because the ASTER global DEMs used to create the synthetic stream networks represent glacier surface elevation rather than estimated deglaciated terrain. All present-day streams within our study region are void of any major dams that inhibit salmon movement based on existing databases of dams55. To summarize present-day stream kms, and all subsequent analyses, we used rstudio: 1.4.1103-4, R: ‘Mirrors’.Identifying and verifying stream gradient thresholds for migrating salmon and for determining accessible glaciersWe used stream gradient-based thresholds the determine constraints in salmon migration and the number of glaciers that would be accessible and create future streams for migrating adult salmon. Based on the large body of literature suggesting stream gradients (e.g., ranging from More

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Synthetic microbial communities (SynComs) constitute an emerging and powerful tool in biological, biomedical, and biotechnological research. Despite recent advances in algorithms for the analysis of culture-independent amplicon sequencing data from microbial communities, there is a lack of tools specifically designed for analyzing SynCom data, where reference sequences for each strain are available. Here we present Rbec, a tool designed for the analysis of SynCom data that accurately corrects PCR and sequencing errors in amplicon sequences and identifies intra-strain polymorphic variation. Extensive evaluation using mock bacterial and fungal communities show that our tool outperforms current methods for samples of varying complexity, diversity, and sequencing depth. Furthermore, Rbec also allows accurate detection of contaminants in SynCom experiments. More

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