The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs

Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (p < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray–Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32, 11.67, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

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The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs

10.20944/preprints202102.0508.v1 ◽

2021 ◽

Author(s):

Feilong Deng ◽

Yushan Li ◽

Xiaoyuan Wei ◽

Xiaofan Wang ◽

Samantha Howe ◽

...

Keyword(s):

Relative Abundance ◽

Antibiotic Resistance Genes ◽

Alpha Diversity ◽

Distance Matrix ◽

Archaeal Community ◽

Gene Families ◽

Shannon Index ◽

Metabolic Potential ◽

Substantial Progress ◽

Archaeal Communities

Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n=76), Denmark (n=100), and France (n=100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (P<0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray-Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus Methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus Methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32%, 11.67%, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being: AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

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The diversity, composition, and metabolic pathways of archaea in pigs

10.21203/rs.3.rs-305488/v1 ◽

2021 ◽

Author(s):

Feilong Deng ◽

Yushan Li ◽

Xiaoyuan Wei ◽

Yingping Xiao ◽

Xiaofan Wang ◽

...

Keyword(s):

Relative Abundance ◽

Antibiotic Resistance Genes ◽

Alpha Diversity ◽

Distance Matrix ◽

Archaeal Community ◽

Gene Families ◽

Shannon Index ◽

Metabolic Potential ◽

Substantial Progress ◽

Archaeal Communities

Abstract Background Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. To this end, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset from the NCBI Sequence Read Archive (SRA) database. Results A total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100) were used in this study. For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (P < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray-Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus Methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus Methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32%, 11.67%, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being: AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Conclusions Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

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Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil

Archaea ◽

10.1155/2015/646820 ◽

2015 ◽

Vol 2015 ◽

pp. 1-11 ◽

Cited By ~ 14

Author(s):

Yendi E. Navarro-Noya ◽

César Valenzuela-Encinas ◽

Alonso Sandoval-Yuriar ◽

Norma G. Jiménez-Bueno ◽

Rodolfo Marsch ◽

...

Keyword(s):

Species Richness ◽

Alpha Diversity ◽

Methanogenic Archaea ◽

Archaeal Community ◽

Soil Samples ◽

Alkaline Soil ◽

Alkaline Soils ◽

Phylogenetic Information ◽

Archaeal Communities ◽

Saline Alkaline Soils

In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC) ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic CandidatusNitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family. Novel phylogenetic branches in the Halobacteriales class were detected in the soil, and more abundantly in soil with the higher pH (10.5), indicating that unknown and uncharacterized Archaea can be found in this soil. Thirteen different genera of the Halobacteriaceae family were identified and were distributed differently between the soils.Halobiforma,Halostagnicola,Haloterrigena, andNatronomonaswere found in all soil samples. Methanogenic archaea were found only in soil with pH between 10.0 and 10.3. Retrieved methanogenic archaea belonged to the Methanosarcinales and Methanomicrobiales orders. The comparison of the archaeal community structures considering phylogenetic information (UniFrac distances) clearly clustered the communities by pH.

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O-143 Characterization of vaginal and endometrial microbiome in patients with chronic endometritis (CE)

Human Reproduction ◽

10.1093/humrep/deab127.011 ◽

2021 ◽

Vol 36 (Supplement_1) ◽

Author(s):

P LOZANO ◽

A Bernabeu ◽

B Lledó ◽

R Morales ◽

F I Aranda ◽

...

Keyword(s):

16S Rrna ◽

Embryo Transfer ◽

Relative Abundance ◽

Beta Diversity ◽

Alpha Diversity ◽

Shannon Index ◽

Small Sample ◽

Diagnostic Methods ◽

Vaginal Microbiome ◽

Chronic Endometritis

Abstract Study question Could vaginal and endometrial microbiome by sequencing 16S rRNA be comparable to classic diagnostic methods or immunohistochemistry CD138 for diagnosis of chronic endometritis? Summary answer A characteristic endometrial and vaginal microbiome is present in patients with chronic endometritis. An abnormal vaginal microbiome correlates with the presence of chronic endometritis. What is known already Chronic endometritis is a disease characterized by persistent inflammation of the endometrial lining. Currently, histopathological evaluation by immunohistochemistry CD138 marker is most common diagnostic method for CE. Microbiome analysis based on subunit 16S rRNA sequencing is a fast tool that can enable the identification of pathogenic microorganisms associated with CE. The main bacteria at vaginal and endometrial level belong to genus Lactobacillus, producers of lactic acid that allows maintaining acidic pH of vagina and acts as barrier against pathogens. Investigations on the effect of an abnormal endometrial and vaginal microbiome could improve assisted reproductive technologies. Study design, size, duration This is a observational pilot study (60 patients and 120 samples). The study population consists of patients attending to our fertility clinic for frozen euploid embryo transfer (FET) from May 2017 to May 2019. Preimplantation Genetic Testing of aneuploidy (PGT-A) was performed at blastocyst stage using Veriseq (Illumina). The inclusion criteria to be meet by patients were: age between 18 and 50 years, own or donated oocytes and use of ICSI. Participants/materials, setting, methods Cohort study with sixty patients undergoing assisted reproductive treatment (TRA) with their own or donated gametes and PGT-A Vaginal and endometrial samples were taken in the cycle prior to embryo transfer. The vaginal and endometrial microbiome was analyzed by mass sequencing of the V3V4 region of 16S rRNA. Bioinformatics analysis was performed using QIIME2 and MicrobiomeAnalyst packages. Alpha, beta diversity and taxonomic characterization were compared with positive and negative CD138 groups for chronic endometritis (CE). Main results and the role of chance Different bacterial communities were detected when vaginal and endometrial samples were analyzed in patients with and without endometritis diagnosed with CD138 immunohistochemistry. In patients with endometritis, a higher alpha diversity index tendency was found in vaginal samples (p = 0.15 for the Shannon index) and significant differences in endometrial samples (p = 0.01 for the Shannon index). In the beta diversity analysis, no significant differences were observed between the groups established as per the diagnosis of endometritis. Vaginal and endometrial samples from women with endometritis showed a microbiome pattern not dominated by Lactobacillus spp. Relative abundance analysis identified the genera Ralstonia and Gardnerella in endometrial sample, and the genera Streptoccoccus and Ureaplasma in vaginal sample of patients diagnosed with CD138 for endometritis. Comparing endometrial and vaginal samples CD138 positive diagnosed for endometritis, alpha diversity (p = 0.06 for the Shannon index and p = 0.08 for the Simpson index) and beta diversity (p < 0.001) showed significant differences. Relative abundance identified the genera Lactobacillus (p = 3.76E-4), Ralstonia (p = 8.19E-4), Delftia (p = 0.004) and Anaerobacillus (p = 0.004) in these sample groups. Limitations, reasons for caution The main limitation of this study is the small sample size. Larger studies including a higher number of samples are needed to confirm the different microbiome pattern observed at the vaginal and endometrial levels in correlation with chronic endometritis. The microbiome pattern has not been analyzed after treatment of CE. Wider implications of the findings Our findings suggest the existence of a characteristic vaginal and endometrial microbiota in patients with chronic endometritis. Different genera and species were identified in patients with and without endometritis depending on whether the sample was endometrial or vaginal. An abnormal vaginal microbiome appears to be strongly correlated with chronic endometritis. Trial registration number Not Applicable

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Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa173 ◽

2020 ◽

Vol 96 (10) ◽

Author(s):

Madangchanok Imchen ◽

Ranjith Kumavath

Keyword(s):

Antibiotic Resistance ◽

Microbial Community ◽

Relative Abundance ◽

Antibiotic Resistance Genes ◽

Alpha Diversity ◽

Mangrove Ecosystem ◽

Mangrove Sediment ◽

Mangrove Forests ◽

Human Intervention ◽

Shotgun Metagenomics

ABSTRACT Saline tolerant mangrove forests partake in vital biogeochemical cycles. However, they are endangered due to deforestation as a result of urbanization. In this study, we have carried out a metagenomic snapshot of the mangrove ecosystem from five countries to assess its taxonomic, functional and antibiotic resistome structure. Chao1 alpha diversity varied significantly (P < 0.001) between the countries (Brazil, Saudi Arabia, China, India and Malaysia). All datasets were composed of 33 phyla dominated by eight major phyla covering >90% relative abundance. Comparative analysis of mangrove with terrestrial and marine ecosystems revealed the strongest heterogeneity in the mangrove microbial community. We also observed that the mangrove community shared similarities to both the terrestrial and marine microbiome, forming a link between the two contrasting ecosystems. The antibiotic resistant genes (ARG) resistome was comprised of nineteen level 3 classifications dominated by multidrug resistance efflux pumps (46.7 ± 4.3%) and BlaR1 family regulatory sensor-transducer disambiguation (25.2 ± 4.8%). ARG relative abundance was significantly higher in Asian countries and in human intervention datasets at a global scale. Our study shows that the mangrove microbial community and its antibiotic resistance are affected by geography as well as human intervention and are unique to the mangrove ecosystem. Understanding changes in the mangrove microbiome and its ARG is significant for sustainable development and public health.

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Fecal Microbiota Diversity in Survivors of Adolescent/Young Adult Hodgkin Lymphoma

Blood ◽

10.1182/blood.v120.21.1533.1533 ◽

2012 ◽

Vol 120 (21) ◽

pp. 1533-1533

Author(s):

Wendy Cozen ◽

Guoqin Yu ◽

Mitchell Gail ◽

Bharat N. Nathwani ◽

Amie E. Hwang ◽

...

Keyword(s):

Young Adult ◽

Gut Microbiota ◽

Hodgkin Lymphoma ◽

Relative Abundance ◽

Alpha Diversity ◽

Fecal Microbiota ◽

Shannon Index ◽

Tree Index ◽

Unique Otus ◽

Whole Tree

Abstract Abstract 1533 Survivors of adolescent/young adult Hodgkin lymphoma (AYAHL) report fewer exposures to infections during childhood compared to controls. They also have persistent genomic and functional aberrations in their lymphocytes that are partially attributable to chemotherapy or radiotherapy. Recent studies have shown that the gut microbiome can affect both the innate and adaptive immune response, and can suppress or exacerbate an inflammatory response. Given the central role of the gut microbiota in immune function, we investigated whether AYAHL survivors, who were members of 13 mono- and dizygotic twin pairs discordant for this disease, have differences in the diversity or phylogenetic configurations of their fecal microbiota compared to their unaffected co-twins. Twin pairs discordant for AYAHL are an ideal study population because they are at least partially matched on genetic and early life factors, both of which influence the composition of the gut microbiome. Pyrosequencing of bacterial 16S rRNA amplicons generated from single fecal samples obtained from each individual yielded 253,182 filtered and de-noised reads translated into species-level operational taxonomic units (OTUs). Standardized across individuals by random sampling, reads were assigned to 2513 OTUs to compare microbiome diversity and relative abundance of taxa. The number of OTU's was compared between twins using a paired student's t-test and a one-way analysis of variance was performed to determine whether such measures differed across twin pairs by comparing the measures between twins to those of randomly paired individuals. AYAHL survivors had less diverse fecal microbial communities compared to their unaffected co-twin controls by all measures of alpha diversity (Table 1). Measures that weighted the relative abundance of the bacteria were not statistically significantly different (Shannon Index, p= 0.270; Chao index, p= 0.066, PD Whole Tree Index, p= 0.051). However, when the unweighted number of unique OTUs was considered, the difference was significant (338 in cases vs. 369 in unaffected co-twin controls, p= 0.015). When the analysis was restricted to OTUs that were present at an abundance of > 0.1% in at least 2 of the 23 samples analyzed, the differences were attenuated, with only the PD Whole Tree index difference in diversity remaining marginally significant (p= 0.045). Only one bacterial taxon was associated with AYAHL, probably due to chance. Phylogenetic measurements indicated that the bacterial component of the microbiota of co-twins were more similar with respect to one another than unrelated individuals, although no differences by zygosity were observed. These results provide evidence that AYAHL survivors have reduced diversity of the gut microbiota, perhaps as a consequence the disease, its treatment, or a particularly hygienic environment. Table 1. Comparisons of alpha diversity measurements between Hodgkin lymphoma cases and co-twin controls. Measurements of Alpha Diversity Mean (Cases) Mean (Unaffected Co-twins) Mean Difference (Unaffected co-twin-case difference) P-value1 Initial analysis No. unique OTUs 338 369 31 0.015 Shannon index 5.6 5.8 0.2 0.27 Chao1 533 574 41 0.066 PD_whole tree 21.2 22.8 1.6 0.051 Conservative analysis No. unique OTUs 183 196 13 0.10 Shannon index 5.2 5.4 0.2 0.40 Chao1 230 237 7 0.47 PD_whole tree 13.7 14.6 0.9 0.045 1 P-value by paired t-tests. Disclosures: No relevant conflicts of interest to declare.

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Behaviors of Homologous Antibiotic Resistance Genes in a Cephalosporin WWTP, Subsequent WWTP and the Receiving River

Frontiers in Environmental Science ◽

10.3389/fenvs.2021.783676 ◽

2021 ◽

Vol 9 ◽

Author(s):

Lei Chen ◽

Mengyu Zhang ◽

Daliang Ning ◽

Joy D Van Nostrand ◽

Yunfeng Yang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Relative Abundance ◽

Resistance Genes ◽

Antibiotic Production ◽

Treatment Plant ◽

Antibiotic Resistance Genes ◽

Gene Families ◽

Selection Pressures ◽

Environmental Selection ◽

Receiving Stream

High concentrations of antibiotics in antibiotic production wastewater can cause the widespread transmission of antibiotic resistance genes (ARGs). Here, we collected a set of time series samples from a cephalosporin production wastewater treatment plant (X-WWTP), the subsequent municipal WWTP (Y-WWTP) and the receiving stream. Using a functional gene microarray, GeoChip 5.0, which contains multiple homologous probes for 18 ARG and 13 antibiotic metabolism gene (AMG) families, we found that more than 50% of homologous probes for 20 gene families showed a relative abundance higher in X-WWTP, while only 10–20% showed lower relative abundance. The different response patterns of homologous ARG (hARGs) within the same ARG family imply environmental selection pressures are only responsible for the ARG enrichment and spread of some specific instead of all ARG-containing microorganisms, which contradicted the traditionally held belief that environmental selection pressures, especially antibiotic concentration, select for all ARG-containing microorganisms thereby selecting different hARGs in the same ARG family in an undifferentiated way. Network results imply that hARGs from three β_lactamase families enriched under the selection pressure of high cephalosporin antibiotic concentrations in X-WWTP formed positively correlated homologous ARG clusters (pohARGCs). The pohARGCs were also enhanced in the sediment of the receiving stream. The enrichment of hARGs from three β_lactamase families was likely through microorganisms belonging to the Betaproteobacteria genus.

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Impact of antibiotics to off-target infant gut microbiota and resistance genes in cohort studies

10.1101/2021.11.02.21265394 ◽

2021 ◽

Author(s):

Rebecca M Lebeaux ◽

Juliette C Madan ◽

Quang P Nguyen ◽

Modupe O Coker ◽

Erika F Dade ◽

...

Keyword(s):

Relative Abundance ◽

Resistance Genes ◽

Respiratory Infections ◽

Antibiotic Resistance Genes ◽

Alpha Diversity ◽

Metagenomic Sequencing ◽

Antibiotic Exposure ◽

Sequencing Data ◽

Compositional Diversity ◽

The Impact

Background: Young children are frequently exposed to antibiotics for otitis media and respiratory infections, with the potential for collateral consequences on the gut microbiome. The impact of antibiotic exposures to off-target microbes (i.e., bacteria not targeted by antibiotic treatment) and antibiotic resistance genes (ARGs) is unknown. Methods: We used metagenomic sequencing data from paired stool samples collected prior to antibiotic exposure and at 1 year from over 200 infants and a difference-in-differences approach to assess the relationship between subsequent exposures and the abundance or compositional diversity of off-target microbes and ARGs while adjusting for covariates. Results: By 1 year, the relative abundance of multiple species and ARGs differed by antibiotic exposure. Compared to infants never exposed to antibiotics, Bacteroides vulgatus relative abundance increased by 1.72% (95%CI:0.19,3.24) while Bacteroides fragilis decreased by 1.56% (95%CI:-4.32,1.21). Bifidobacterium species also exhibited opposing trends suggesting differential antibiotic selection. Overall, antibiotic exposure was associated with a dose-dependent decrease in alpha diversity of off-target microbes. ARGs associated with antibiotic exposure included class A beta-lactamase gene CfxA6. Among infants attending day care, Escherichia coli and ARG abundance were both positively associated with antibiotic use. Conclusion: Further quantifying impacts to off-target microbes and ARGs has implications for antibiotic stewardship

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Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

Genome Biology ◽

10.1186/s13059-019-1831-z ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 14

Author(s):

Robert C. Kaplan ◽

Zheng Wang ◽

Mykhaylo Usyk ◽

Daniela Sotres-Alvarez ◽

Martha L. Daviglus ◽

...

Keyword(s):

Community Health ◽

Gut Microbiome ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Shannon Index ◽

Health Study ◽

Rrna Gene ◽

Cross Sectional ◽

Hispanic Community ◽

The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

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Unraveling the Metabolic Potential of Asgardarchaeota in a Sediment from the Mediterranean Hydrocarbon-Contaminated Water Basin Mar Piccolo (Taranto, Italy)

Microorganisms ◽

10.3390/microorganisms9040859 ◽

2021 ◽

Vol 9 (4) ◽

pp. 859

Author(s):

Andrea Firrincieli ◽

Andrea Negroni ◽

Giulio Zanaroli ◽

Martina Cappelletti

Keyword(s):

Archaeal Community ◽

Hydrocarbon Biodegradation ◽

Natural Ecosystems ◽

Central Mediterranean ◽

Metabolic Potential ◽

Metabolic Role ◽

Sequencing Studies ◽

Terrestrial Environments ◽

Metagenome Sequencing ◽

Aliphatic And Aromatic Hydrocarbons

Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in both marine and terrestrial environments. In this work, we focused our study on the metagenomic characterization of the archaeal community inhabiting the Mar Piccolo (Taranto, Italy, central Mediterranean) sediments heavily contaminated by petroleum hydrocarbons and polychlorinated biphenyls (PCB). Among metagenomic bins reconstructed from Mar Piccolo microbial community, we have identified members of the Asgardarchaeota superphylum that has been recently proposed to play a central role in hydrocarbon cycling in natural ecosystems under anoxic conditions. In particular, we found members affiliated with Thorarchaeota, Heimdallarchaeota, and Lokiarchaeota phyla and analyzed their genomic potential involved in central metabolism and hydrocarbon biodegradation. Metabolic prediction based on metagenomic analysis identified the malonyl-CoA and benzoyl-CoA routes as the pathways involved in aliphatic and aromatic biodegradation in these Asgardarchaeota members. This is the first study to give insight into the archaeal community functionality and connection to hydrocarbon degradation in marine sediment historically contaminated by hydrocarbons.

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