Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying ...its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we perform high-resolution metagenomic-based analyzes of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in human populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny between microbes and hosts are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids. We find that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.
Seafloor methane release can significantly affect the global carbon cycle and climate. Appreciable quantities of methane are stored in continental margin sediments as shallow gas and hydrate ...deposits, and changes in pressure, temperature and/or bottom-currents can liberate significant amounts of this greenhouse gas. Understanding the spatial and temporal dynamics of marine methane deposits and their relationships to environmental change are critical for assessing past and future carbon cycle and climate change. Here we present foraminiferal stable carbon isotope and sediment mineralogy records suggesting for the first time that seafloor methane release occurred along the southern Brazilian margin during the last glacial period (40-20 cal ka BP). Our results show that shallow gas deposits on the southern Brazilian margin responded to glacial-interglacial paleoceanographic changes releasing methane due to the synergy of sea level lowstand, warmer bottom waters and vigorous bottom currents during the last glacial period. High sea level during the Holocene resulted in an upslope shift of the Brazil Current, cooling the bottom waters and reducing bottom current strength, reducing methane emissions from the southern Brazilian margin.
To influence host and disease phenotype, compositional microbiome changes, which have been demonstrated in patients with primary sclerosing cholangitis (PSC), must be accompanied by functional ...changes. We therefore aimed to characterize the genetic potential of the gut microbiome in patients with PSC compared with healthy controls (HCs) and patients with inflammatory bowel disease (IBD).
Fecal DNA from 2 cohorts (1 Norwegian and 1 German), in total comprising 136 patients with PSC (58% with IBD), 158 HCs, and 93 patients with IBD without PSC, were subjected to metagenomic shotgun sequencing, generating 17 billion paired-end sequences, which were processed using HUMAnN2 and MetaPhlAn2, and analyzed using generalized linear models and random effects meta-analyses.
Patients with PSC had fewer microbial genes compared with HCs (P < .0001). Compared with HCs, patients with PSC showed enrichment and increased prevalence of Clostridium species and a depletion of, for example, Eubacterium spp and Ruminococcus obeum. Patients with PSC showed marked differences in the abundance of genes related to vitamin B6 synthesis and branched-chain amino acid synthesis (Qfdr < .05). Targeted metabolomics of plasma from an independent set of patients with PSC and controls found reduced concentrations of vitamin B6 and branched-chain amino acids in PSC (P < .0001), which strongly associated with reduced liver transplantation–free survival (log-rank P < .001). No taxonomic or functional differences were detected between patients with PSC with and without IBD.
The gut microbiome in patients with PSC exhibits large functional differences compared with that in HCs, including microbial metabolism of essential nutrients. Alterations in related circulating metabolites associated with disease course, suggesting that microbial functions may be relevant for the disease process in PSC.
Obesity and type 2 diabetes (T2D) are metabolic disorders that are linked to microbiome alterations. However, their co-occurrence poses challenges in disentangling microbial features unique to each ...condition. We analyzed gut microbiomes of lean non-diabetic (n = 633), obese non-diabetic (n = 494), and obese individuals with T2D (n = 153) from German population and metabolic disease cohorts. Microbial taxonomic and functional profiles were analyzed along with medical histories, serum metabolomics, biometrics, and dietary data. Obesity was associated with alterations in microbiome composition, individual taxa, and functions with notable changes in Akkermansia, Faecalibacterium, Oscillibacter, and Alistipes, as well as in serum metabolites that correlated with gut microbial patterns. However, microbiome associations were modest for T2D, with nominal increases in Escherichia/Shigella. Medications, including antihypertensives and antidiabetics, along with dietary supplements including iron, were significantly associated with microbiome variation. These results differentiate microbial components of these interrelated metabolic diseases and identify dietary and medication exposures to consider in future studies.
Display omitted
•Obesity, but not type 2 diabetes, associated with gut microbiome variation•Medications and dietary supplements associated with gut microbiome variation•High iron intake affected microbiome composition in mice•Microbiome variation was also reflected in serum metabolite profiles
Co-occurrence of obesity and type 2 diabetes poses challenges in assessing microbiota changes specific to each condition. By comparing gut microbiomes of lean, obese non-diabetic, and obese type 2 diabetic individuals, Thingholm et al. found that obesity, unlike type 2 diabetes, was associated with microbiome variation. Medications and dietary supplements were further linked to microbiota alterations.
Manganese nodules of the Clarion–Clipperton Fracture Zone (CCFZ) in the NE Pacific Ocean are highly enriched in Ni, Cu, Co, Mo and rare-earth elements, and thus may be the subject of future mining ...operations. Elucidating the depositional and biogeochemical processes that contribute to nodule formation, as well as the respective redox environment, in both water column and sediment, supports our ability to locate future nodule deposits and to evaluate the potential ecological and environmental effects of future deep-sea mining. For these purposes we studied the local hydrodynamics and pore-water geochemistry with respect to the nodule coverage at four sites in the eastern CCFZ. Furthermore, we carried out selective leaching experiments at these sites in order to assess the potential mobility of Mn in the solid phase, and compared them with the spatial variations in sedimentation rates. We found that the oxygen penetration depth is 180–300cm at all four sites, while reduction of Mn and NO3− is only significant below the oxygen penetration depth at sites with small or no nodules on the sediment surface. At the site without nodules, potential microbial respiration rates, determined by incubation experiments using 14C-labeled acetate, are slightly higher than at sites with nodules. Leaching experiments showed that surface sediments covered with big or medium-sized nodules are enriched in mobilizable Mn. Our deep oxygen measurements and pore-water data suggest that hydrogenetic and oxic-diagenetic processes control the present-day nodule growth at these sites, since free manganese from deeper sediments is unable to reach the sediment surface. We propose that the observed strong lateral contrasts in nodule size and abundance are sensitive to sedimentation rates, which in turn, are controlled by small-scale variations in seafloor topography and bottom-water current intensity.
•We evaluated the pore-water geochemistry with respect to nodule coverage in the CCFZ.•We found that hydrogenetic and oxic-diagenetic processes control the present-day nodule growth.•Surface sediments covered with big or medium-sized nodules are enriched in mobilizable Mn.
We present a global atlas of downcore foraminiferal oxygen and carbon isotope ratios available at https://doi.org/10.1594/PANGAEA.936747
(Mulitza et al., 2021a). The database contains 2106 published ...and previously unpublished stable isotope downcore records with 361 949 stable isotope
values of various planktic and benthic species of Foraminifera from 1265 sediment cores. Age constraints are provided by 6153 uncalibrated
radiocarbon ages from 598 (47 %) of the cores. Each stable isotope and radiocarbon series is provided in a separate netCDF file containing
fundamental metadata as attributes. The data set can be managed and explored with the free software tool PaleoDataView. The atlas will provide
important data for paleoceanographic analyses and compilations, site surveys, or for teaching marine stratigraphy. The database can be updated with
new records as they are generated, providing a live ongoing resource into the future.
The role of the human gut microbiome in colorectal cancer (CRC) is unclear as most studies on the topic are unable to discern correlation from causation. We apply two-sample Mendelian randomization ...(MR) to estimate the causal relationship between the gut microbiome and CRC. We used summary-level data from independent genome-wide association studies to estimate the causal effect of 14 microbial traits (n = 3890 individuals) on overall CRC (55,168 cases, 65,160 controls) and site-specific CRC risk, conducting several sensitivity analyses to understand the nature of results. Initial MR analysis suggested that a higher abundance of Bifidobacterium and presence of an unclassified group of bacteria within the Bacteroidales order in the gut increased overall and site-specific CRC risk. However, sensitivity analyses suggested that instruments used to estimate relationships were likely complex and involved in many potential horizontal pleiotropic pathways, demonstrating that caution is needed when interpreting MR analyses with gut microbiome exposures. In assessing reverse causality, we did not find strong evidence that CRC causally affected these microbial traits. Whilst our study initially identified potential causal roles for two microbial traits in CRC, importantly, further exploration of these relationships highlighted that these were unlikely to reflect causality.
PDF
