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ABSTRACT Dietary polyphenols can significantly benefit human health, but their bioavailability is metabolically controlled by human gut microbiota. To facilitate the study of polyphenol metabolism for human gut health, we have manually curated experimentally characterized polyphenol utilization proteins (PUPs) from published literature. This resulted in 60 experimentally characterized PUPs (named seeds) with various metadata, such as species and substrate. Further database search found 107,851 homologs of the seeds from UniProt and UHGP (unified human gastrointestinal protein) databases. All PUP seeds and homologs were classified into protein classes, families, and subfamilies based on Enzyme Commission (EC) numbers, Pfam (protein family) domains, and sequence similarity networks. By locating PUP homologs in the genomes of UHGP, we have identified 1,074 physically linked PUP gene clusters (PGCs), which are potentially involved in polyphenol metabolism in the human gut. The gut microbiome of Africans was consistently ranked the top in terms of the abundance and prevalence of PUP homologs and PGCs among all geographical continents. This reflects the fact that dietary polyphenols are consumed by the African population more commonly than by other populations, such as Europeans and North Americans. A case study of the Hadza hunter-gatherer microbiome verified the feasibility of using dbPUP to profile metagenomic data for biologically meaningful discovery, suggesting an association between diet and PUP abundance. A Pfam domain enrichment analysis of PGCs identified a number of putatively novel PUP families. Lastly, a user-friendly web interface ( https://bcb.unl.edu/dbpup/ ) provides all the data online to facilitate the research of polyphenol metabolism for improved human health. IMPORTANCE Long-term consumption of polyphenol-rich foods has been shown to lower the risk of various human diseases, such as cardiovascular diseases, cancers, and metabolic diseases. Raw polyphenols are often enzymatically processed by gut microbiome, which contains various polyphenol utilization proteins (PUPs) to produce metabolites with much higher bioaccessibility to gastrointestinal cells. This study delivered dbPUP as an online database for experimentally characterized PUPs and their homologs in human gut microbiome. This work also performed a systematic classification of PUPs into enzyme classes, families, and subfamilies. The signature Pfam domains were identified for PUP families, enabling conserved domain-based PUP annotation. This standardized sequence similarity-based PUP classification system offered a guideline for the future inclusion of new experimentally characterized PUPs and the creation of new PUP families. An in-depth data analysis was further conducted on PUP homologs and physically linked PUP gene clusters (PGCs) in gut microbiomes of different human populations. 

Abstract PULs (polysaccharide utilization loci) are discrete gene clusters of CAZymes (Carbohydrate Active EnZymes) and other genes that work together to digest and utilize carbohydrate substrates. While PULs have been extensively characterized in Bacteroidetes, there exist PULs from other bacterial phyla, as well as archaea and metagenomes, that remain to be catalogued in a database for efficient retrieval. We have developed an online database dbCAN-PUL (http://bcb.unl.edu/dbCAN_PUL/) to display experimentally verified CAZyme-containing PULs from literature with pertinent metadata, sequences, and annotation. Compared to other online CAZyme and PUL resources, dbCAN-PUL has the following new features: (i) Batch download of PUL data by target substrate, species/genome, genus, or experimental characterization method; (ii) Annotation for each PUL that displays associated metadata such as substrate(s), experimental characterization method(s) and protein sequence information, (iii) Links to external annotation pages for CAZymes (CAZy), transporters (UniProt) and other genes, (iv) Display of homologous gene clusters in GenBank sequences via integrated MultiGeneBlast tool and (v) An integrated BLASTX service available for users to query their sequences against PUL proteins in dbCAN-PUL. With these features, dbCAN-PUL will be an important repository for CAZyme and PUL research, complementing our other web servers and databases (dbCAN2, dbCAN-seq). 

Abstract. Accurate assessment of anthropogenic carbon dioxide (CO2) emissions andtheir redistribution among the atmosphere, ocean, and terrestrial biospherein a changing climate is critical to better understand the global carboncycle, support the development of climate policies, and project futureclimate change. Here we describe and synthesize data sets and methodologies toquantify the five major components of the global carbon budget and theiruncertainties. Fossil CO2 emissions (EFOS) are based on energystatistics and cement production data, while emissions from land-use change(ELUC), mainly deforestation, are based on land use and land-use changedata and bookkeeping models. Atmospheric CO2 concentration is measureddirectly, and its growth rate (GATM) is computed from the annualchanges in concentration. The ocean CO2 sink (SOCEAN) is estimatedwith global ocean biogeochemistry models and observation-baseddata products. The terrestrial CO2 sink (SLAND) is estimated withdynamic global vegetation models. The resulting carbon budget imbalance(BIM), the difference between the estimated total emissions and theestimated changes in the atmosphere, ocean, and terrestrial biosphere, is ameasure of imperfect data and understanding of the contemporary carboncycle. All uncertainties are reported as ±1σ. For the year 2021, EFOS increased by 5.1 % relative to 2020, withfossil emissions at 10.1 ± 0.5 GtC yr−1 (9.9 ± 0.5 GtC yr−1 when the cement carbonation sink is included), and ELUC was 1.1 ± 0.7 GtC yr−1, for a total anthropogenic CO2 emission(including the cement carbonation sink) of 10.9 ± 0.8 GtC yr−1(40.0 ± 2.9 GtCO2). Also, for 2021, GATM was 5.2 ± 0.2 GtC yr−1 (2.5 ± 0.1 ppm yr−1), SOCEAN was 2.9  ± 0.4 GtC yr−1, and SLAND was 3.5 ± 0.9 GtC yr−1, with aBIM of −0.6 GtC yr−1 (i.e. the total estimated sources were too low orsinks were too high). The global atmospheric CO2 concentration averaged over2021 reached 414.71 ± 0.1 ppm. Preliminary data for 2022 suggest anincrease in EFOS relative to 2021 of +1.0 % (0.1 % to 1.9 %)globally and atmospheric CO2 concentration reaching 417.2 ppm, morethan 50 % above pre-industrial levels (around 278 ppm). Overall, the meanand trend in the components of the global carbon budget are consistentlyestimated over the period 1959–2021, but discrepancies of up to 1 GtC yr−1 persist for the representation of annual to semi-decadalvariability in CO2 fluxes. Comparison of estimates from multipleapproaches and observations shows (1) a persistent large uncertainty in theestimate of land-use change emissions, (2) a low agreement between thedifferent methods on the magnitude of the land CO2 flux in the northernextratropics, and (3) a discrepancy between the different methods on thestrength of the ocean sink over the last decade. This living data updatedocuments changes in the methods and data sets used in this new globalcarbon budget and the progress in understanding of the global carbon cyclecompared with previous publications of this data set. The data presented inthis work are available at https://doi.org/10.18160/GCP-2022 (Friedlingstein et al., 2022b). 

Abstract. Accurate assessment of anthropogenic carbon dioxide(CO2) emissions and their redistribution among the atmosphere,ocean, and terrestrial biosphere – the “global carbon budget” – isimportant to better understand the global carbon cycle, support thedevelopment of climate policies, and project future climate change. Here wedescribe data sets and methodology to quantify the five major components ofthe global carbon budget and their uncertainties. Fossil CO2emissions (EFF) are based on energy statistics and cementproduction data, while emissions from land use and land-use change (ELUC),mainly deforestation, are based on land use and land-use change data andbookkeeping models. Atmospheric CO2 concentration is measureddirectly and its growth rate (GATM) is computed from the annualchanges in concentration. The ocean CO2 sink (SOCEAN)and terrestrial CO2 sink (SLAND) are estimated withglobal process models constrained by observations. The resulting carbonbudget imbalance (BIM), the difference between the estimatedtotal emissions and the estimated changes in the atmosphere, ocean, andterrestrial biosphere, is a measure of imperfect data and understanding ofthe contemporary carbon cycle. All uncertainties are reported as ±1σ. For the last decade available (2008–2017), EFF was9.4±0.5 GtC yr−1, ELUC 1.5±0.7 GtC yr−1, GATM 4.7±0.02 GtC yr−1,SOCEAN 2.4±0.5 GtC yr−1, and SLAND 3.2±0.8 GtC yr−1, with a budget imbalance BIM of0.5 GtC yr−1 indicating overestimated emissions and/or underestimatedsinks. For the year 2017 alone, the growth in EFF was about 1.6 %and emissions increased to 9.9±0.5 GtC yr−1. Also for 2017,ELUC was 1.4±0.7 GtC yr−1, GATM was 4.6±0.2 GtC yr−1, SOCEAN was 2.5±0.5 GtC yr−1, and SLAND was 3.8±0.8 GtC yr−1,with a BIM of 0.3 GtC. The global atmosphericCO2 concentration reached 405.0±0.1 ppm averaged over 2017.For 2018, preliminary data for the first 6–9 months indicate a renewedgrowth in EFF of +2.7 % (range of 1.8 % to 3.7 %) basedon national emission projections for China, the US, the EU, and India andprojections of gross domestic product corrected for recent changes in thecarbon intensity of the economy for the rest of the world. The analysispresented here shows that the mean and trend in the five components of theglobal carbon budget are consistently estimated over the period of 1959–2017,but discrepancies of up to 1 GtC yr−1 persist for the representationof semi-decadal variability in CO2 fluxes. A detailed comparisonamong individual estimates and the introduction of a broad range ofobservations show (1) no consensus in the mean and trend in land-use changeemissions, (2) a persistent low agreement among the different methods onthe magnitude of the land CO2 flux in the northern extra-tropics,and (3) an apparent underestimation of the CO2 variability by oceanmodels, originating outside the tropics. This living data update documentschanges in the methods and data sets used in this new global carbon budgetand the progress in understanding the global carbon cycle compared withprevious publications of this data set (Le Quéré et al., 2018, 2016,2015a, b, 2014, 2013). All results presented here can be downloaded fromhttps://doi.org/10.18160/GCP-2018.