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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. Understanding and quantifying the global methane (CH4) budget is important for assessing realistic pathways to mitigate climate change. Emissions and atmospheric concentrations of CH4 continue to increase, maintaining CH4 as the second most important human-influenced greenhouse gas in terms of climate forcing after carbon dioxide (CO2). The relative importance of CH4 compared to CO2 for temperature change is related to its shorter atmospheric lifetime, stronger radiative effect, and acceleration in atmospheric growth rate over the past decade, the causes of which are still debated. Two major challenges in reducing uncertainties in the factors explaining the well-observed atmospheric growth rate arise from diverse, geographically overlapping CH4 sources and from the uncertain magnitude and temporal change in the destruction of CH4 by short-lived and highly variable hydroxyl radicals (OH). To address these challenges, we have established a consortium of multi-disciplinary scientists under the umbrella of the Global Carbon Project to improve, synthesise and update the global CH4 budget regularly and to stimulate new research on the methane cycle. Following Saunois et al. (2016, 2020), we present here the third version of the living review paper dedicated to the decadal CH4 budget, integrating results of top-down CH4 emission estimates (based on in-situ and greenhouse gas observing satellite (GOSAT) atmospheric observations and an ensemble of atmospheric inverse-model results) and bottom-up estimates (based on process-based models for estimating land-surface emissions and atmospheric chemistry, inventories of anthropogenic emissions, and data-driven extrapolations). We present a budget for the most recent 2010–2019 calendar decade (the latest period for which full datasets are available), for the previous decade of 2000–2009 and for the year 2020. The revision of the bottom-up budget in this edition benefits from important progress in estimating inland freshwater emissions, with better accounting of emissions from lakes and ponds, reservoirs, and streams and rivers. This budget also reduces double accounting across freshwater and wetland emissions and, for the first time, includes an estimate of the potential double accounting that still exists (average of 23 Tg CH4 yr-1). Bottom-up approaches show that the combined wetland and inland freshwater emissions average 248 [159–369] Tg CH4 yr-1 for the 2010–2019 decade. Natural fluxes are perturbed by human activities through climate, eutrophication, and land use. In this budget, we also estimate, for the first time, this anthropogenic component contributing to wetland and inland freshwater emissions. Newly available gridded products also allowed us to derive an almost complete latitudinal and regional budget based on bottom-up approaches. For the 2010–2019 decade, global CH4 emissions are estimated by atmospheric inversions (top-down) to be 575 Tg CH4 yr-1 (range 553–586, corresponding to the minimum and maximum estimates of the model ensemble). Of this amount, 369 Tg CH4 yr-1 or ~65 % are attributed to direct anthropogenic sources in the fossil, agriculture and waste and anthropogenic biomass burning (range 350–391 Tg CH4 yr-1 or 63–68 %). For the 2000–2009 period, the atmospheric inversions give a slightly lower total emission than for 2010–2019, by 32 Tg CH4 yr-1 (range 9–40). Since 2012, global direct anthropogenic CH4 emission trends have been tracking scenarios that assume no or minimal climate mitigation policies proposed by the Intergovernmental Panel on Climate Change (shared socio-economic pathways SSP5 and SSP3). Bottom-up methods suggest 16 % (94 Tg CH4 yr-1) larger global emissions (669 Tg CH4 yr-1, range 512–849) than top-down inversion methods for the 2010–2019 period. The discrepancy between the bottom-up and the top-down budgets has been greatly reduced compared to the previous differences (167 and 156 Tg CH4 yr-1 in Saunois et al. (2016, 2020), respectively), and for the first time uncertainty in bottom-up and top-down budgets overlap. The latitudinal distribution from atmospheric inversion-based emissions indicates a predominance of tropical and southern hemisphere emissions (~65 % of the global budget, <30° N) compared to mid (30° N–60° N, ~30 % of emissions) and high-northern latitudes (60° N–90° N, ~4 % of global emissions). This latitudinal distribution is similar in the bottom-up budget though the bottom-up budget estimates slightly larger contributions for the mid and high-northern latitudes, and slightly smaller contributions from the tropics and southern hemisphere than the inversions. Although differences have been reduced between inversions and bottom-up, the most important source of uncertainty in the global CH4 budget is still attributable to natural emissions, especially those from wetlands and inland freshwaters. We identify five major priorities for improving the CH4 budget: i) producing a global, high-resolution map of water-saturated soils and inundated areas emitting CH4 based on a robust classification of different types of emitting ecosystems; ii) further development of process-based models for inland-water emissions; iii) intensification of CH4 observations at local (e.g., FLUXNET-CH4 measurements, urban-scale monitoring, satellite imagery with pointing capabilities) to regional scales (surface networks and global remote sensing measurements from satellites) to constrain both bottom-up models and atmospheric inversions; iv) improvements of transport models and the representation of photochemical sinks in top-down inversions, and v) integration of 3D variational inversion systems using isotopic and/or co-emitted species such as ethane as well as information in the bottom-up inventories on anthropogenic super-emitters detected by remote sensing (mainly oil and gas sector but also coal, agriculture and landfills) to improve source partitioning. The data presented here can be downloaded from https://doi.org/10.18160/GKQ9-2RHT (Martinez et al., 2024). 

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 and their redistribution among the atmosphere, ocean, and terrestrial biosphere in a changing climate is critical to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe and synthesize data sets and methodology to quantify the five major components of the global carbon budget and their uncertainties. Fossil CO2 emissions (EFOS) are based on energy statistics and cement production data, while emissions from land-use change (ELUC), mainly deforestation, are based on land-use and land-use change data and bookkeeping models. Atmospheric CO2 concentration is measured directly, and its growth rate (GATM) is computed from the annual changes in concentration. The ocean CO2 sink (SOCEAN) is estimated with global ocean biogeochemistry models and observation-based fCO2 products. The terrestrial CO2 sink (SLAND) is estimated with dynamic global vegetation models. Additional lines of evidence on land and ocean sinks are provided by atmospheric inversions, atmospheric oxygen measurements, and Earth system models. The resulting carbon budget imbalance (BIM), the difference between the estimated total emissions and the estimated changes in the atmosphere, ocean, and terrestrial biosphere, is a measure of imperfect data and incomplete understanding of the contemporary carbon cycle. All uncertainties are reported as ±1σ. For the year 2022, EFOS increased by 0.9 % relative to 2021, with fossil emissions at 9.9±0.5 Gt C yr−1 (10.2±0.5 Gt C yr−1 when the cement carbonation sink is not included), and ELUC was 1.2±0.7 Gt C yr−1, for a total anthropogenic CO2 emission (including the cement carbonation sink) of 11.1±0.8 Gt C yr−1 (40.7±3.2 Gt CO2 yr−1). Also, for 2022, GATM was 4.6±0.2 Gt C yr−1 (2.18±0.1 ppm yr−1; ppm denotes parts per million), SOCEAN was 2.8±0.4 Gt C yr−1, and SLAND was 3.8±0.8 Gt C yr−1, with a BIM of −0.1 Gt C yr−1 (i.e. total estimated sources marginally too low or sinks marginally too high). The global atmospheric CO2 concentration averaged over 2022 reached 417.1±0.1 ppm. Preliminary data for 2023 suggest an increase in EFOS relative to 2022 of +1.1 % (0.0 % to 2.1 %) globally and atmospheric CO2 concentration reaching 419.3 ppm, 51 % above the pre-industrial level (around 278 ppm in 1750). Overall, the mean of and trend in the components of the global carbon budget are consistently estimated over the period 1959–2022, with a near-zero overall budget imbalance, although discrepancies of up to around 1 Gt C yr−1 persist for the representation of annual to semi-decadal variability in CO2 fluxes. Comparison of estimates from multiple approaches and observations shows the following: (1) a persistent large uncertainty in the estimate of land-use changes emissions, (2) a low agreement between the different methods on the magnitude of the land CO2 flux in the northern extra-tropics, and (3) a discrepancy between the different methods on the strength of the ocean sink over the last decade. This living-data update documents changes in methods and data sets applied to this most recent global carbon budget as well as evolving community understanding of the global carbon cycle. The data presented in this work are available at https://doi.org/10.18160/GCP-2023 (Friedlingstein et al., 2023). 

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. Understanding and quantifying the global methane (CH4) budgetis important for assessing realistic pathways to mitigate climate change.Atmospheric emissions and concentrations of CH4 continue to increase,making CH4 the second most important human-influenced greenhouse gas interms of climate forcing, after carbon dioxide (CO2). The relativeimportance of CH4 compared to CO2 depends on its shorteratmospheric lifetime, stronger warming potential, and variations inatmospheric growth rate over the past decade, the causes of which are stilldebated. Two major challenges in reducing uncertainties in the atmosphericgrowth rate arise from the variety of geographically overlapping CH4sources and from the destruction of CH4 by short-lived hydroxylradicals (OH). To address these challenges, we have established aconsortium of multidisciplinary scientists under the umbrella of the GlobalCarbon Project to synthesize and stimulate new research aimed at improvingand regularly updating the global methane budget. Following Saunois et al. (2016), we present here the second version of the living review paperdedicated to the decadal methane budget, integrating results of top-downstudies (atmospheric observations within an atmospheric inverse-modellingframework) and bottom-up estimates (including process-based models forestimating land surface emissions and atmospheric chemistry, inventories ofanthropogenic emissions, and data-driven extrapolations). For the 2008–2017 decade, global methane emissions are estimated byatmospheric inversions (a top-down approach) to be 576 Tg CH4 yr−1 (range 550–594, corresponding to the minimum and maximumestimates of the model ensemble). Of this total, 359 Tg CH4 yr−1 or∼ 60 % is attributed to anthropogenic sources, that isemissions caused by direct human activity (i.e. anthropogenic emissions; range 336–376 Tg CH4 yr−1 or 50 %–65 %). The mean annual total emission for the new decade (2008–2017) is29 Tg CH4 yr−1 larger than our estimate for the previous decade (2000–2009),and 24 Tg CH4 yr−1 larger than the one reported in the previousbudget for 2003–2012 (Saunois et al., 2016). Since 2012, global CH4emissions have been tracking the warmest scenarios assessed by theIntergovernmental Panel on Climate Change. Bottom-up methods suggest almost30 % larger global emissions (737 Tg CH4 yr−1, range 594–881)than top-down inversion methods. Indeed, bottom-up estimates for naturalsources such as natural wetlands, other inland water systems, and geologicalsources are higher than top-down estimates. The atmospheric constraints onthe top-down budget suggest that at least some of these bottom-up emissionsare overestimated. The latitudinal distribution of atmosphericobservation-based emissions indicates a predominance of tropical emissions(∼ 65 % of the global budget, < 30∘ N)compared to mid-latitudes (∼ 30 %, 30–60∘ N)and high northern latitudes (∼ 4 %, 60–90∘ N). The most important source of uncertainty in the methanebudget is attributable to natural emissions, especially those from wetlandsand other inland waters. Some of our global source estimates are smaller than those in previouslypublished budgets (Saunois et al., 2016; Kirschke et al., 2013). In particular wetland emissions are about 35 Tg CH4 yr−1 lower due toimproved partition wetlands and other inland waters. Emissions fromgeological sources and wild animals are also found to be smaller by 7 Tg CH4 yr−1 by 8 Tg CH4 yr−1, respectively. However, the overalldiscrepancy between bottom-up and top-down estimates has been reduced byonly 5 % compared to Saunois et al. (2016), due to a higher estimate of emissions from inland waters, highlighting the need for more detailed research on emissions factors. Priorities for improving the methanebudget include (i) a global, high-resolution map of water-saturated soilsand inundated areas emitting methane based on a robust classification ofdifferent types of emitting habitats; (ii) further development ofprocess-based models for inland-water emissions; (iii) intensification ofmethane observations at local scales (e.g., FLUXNET-CH4 measurements)and urban-scale monitoring to constrain bottom-up land surface models, andat regional scales (surface networks and satellites) to constrainatmospheric inversions; (iv) improvements of transport models and therepresentation of photochemical sinks in top-down inversions; and (v) development of a 3D variational inversion system using isotopic and/orco-emitted species such as ethane to improve source partitioning. The data presented here can be downloaded fromhttps://doi.org/10.18160/GCP-CH4-2019 (Saunois et al., 2020) and from theGlobal Carbon Project.