Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota DOI Creative Commons
David Bars‐Cortina, Elies Ramon, Blanca Rius‐Sansalvador

et al.

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: July 29, 2024

Abstract Background Gut dysbiosis has been associated with colorectal cancer (CRC), the third most prevalent in world. This study compares microbiota taxonomic and abundance results obtained by 16S rRNA gene sequencing (16S) whole shotgun metagenomic to investigate their reliability for bacteria profiling. The experimental design included 156 human stool samples from healthy controls, advanced (high-risk) lesion patients (HRL), CRC cases, each sample sequenced using both methods. We thoroughly compared technologies at species, genus, family annotation levels, differences these taxa, sparsity, alpha beta diversities, ability train prediction models, similarity of microbial signature derived models. Results As expected, showed that detects only part gut community revealed shotgun, although some genera were profiled 16S. data was sparser exhibited lower diversity. In ranks, highly differed, partially due a disagreement reference databases. When considering shared positively correlated between two strategies. also found moderate correlation alpha-diversity measures, as well PCoAs. Regarding machine learning models degree predictive power an independent test set, but we could not demonstrate clear superiority one technology over other. Microbial signatures techniques taxa previously development, e.g., Parvimonas micra . Conclusions Shotgun provide different lenses examine communities. While have demonstrated they can unravel common patterns (including signatures), often gives more detailed snapshot than 16S, depth breadth. Instead, will tend show picture, giving greater weight dominant sample. Therefore, recommend choosing or another technique before launching study. Specifically, is preferred microbiome in-depth analyses, while suitable tissue studies targeted aims.

Language: Английский

A highly conserved core bacterial microbiota with nitrogen-fixation capacity inhabits the xylem sap in maize plants DOI Creative Commons
Liyu Zhang, Meiling Zhang,

Shuyu Huang

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: June 11, 2022

Microbiomes are important for crop performance. However, a deeper knowledge of crop-associated microbial communities is needed to harness beneficial host-microbe interactions. Here, by assessing the assembly and functions maize microbiomes across soil types, climate zones, genotypes, we found that stem xylem selectively recruits highly conserved microbes dominated Gammaproteobacteria. We showed proportion bacterial taxa carrying nitrogenase gene (nifH) was larger in than other organs such as root leaf endosphere. Of 25 core identified sap, several isolated strains were confirmed be active nitrogen-fixers or assist with biological nitrogen fixation. On this basis, established synthetic (SynComs) consisting two diazotrophs helpers. GFP-tagged 15N isotopic dilution method demonstrated these SynComs do thrive contribute, through fixation, 11.8% total N accumulated stems. These sap represent an untapped resource can exploited increase productivity.

Language: Английский

Citations

129
No evidence for a common blood microbiome based on a population study of 9,770 healthy humans DOI Creative Commons
Cedric C.S. Tan, Karrie Kwan Ki Ko, Hui Chen

et al.

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(5), P. 973 - 985

Published: March 30, 2023

Abstract Human blood is conventionally considered sterile but recent studies suggest the presence of a microbiome in healthy individuals. Here we characterized DNA signatures microbes 9,770 individuals using sequencing data from multiple cohorts. After filtering for contaminants, identified 117 microbial species blood, some which had replication. They were primarily commensals associated with gut ( n = 40), mouth 32) and genitourinary tract 18), distinct pathogens detected hospital cultures. No 84% individuals, while remainder only median one species. Less than 5% shared same species, no co-occurrence patterns between different observed associations host phenotypes found. Overall, these results do not support hypothesis consistent core endogenous to human blood. Rather, our findings transient sporadic translocation commensal other body sites into bloodstream.

Language: Английский

Citations

77
The gut commensal Blautia maintains colonic mucus function under low-fiber consumption through secretion of short-chain fatty acids DOI Creative Commons
Sandra Holmberg, R Feeney, V. K.

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: April 25, 2024

Abstract Beneficial gut bacteria are indispensable for developing colonic mucus and fully establishing its protective function against intestinal microorganisms. Low-fiber diet consumption alters the bacterial configuration disturbs this microbe-mucus interaction, but specific microbial metabolites responsible maintaining remain poorly understood. By using human-to-mouse microbiota transplantation ex vivo analysis of function, we here show as a proof-of-concept that individuals who increase their daily dietary fiber intake can improve capacity to prevent diet-mediated defects. Mucus growth, critical feature intact mucus, correlated with abundance commensal Blautia , supplementation coccoides mice confirmed mucus-stimulating capacity. Mechanistically, B. stimulated growth through production short-chain fatty acids propionate acetate via activation acid receptor Ffar2, which could serve new target restore during mucus-associated lifestyle diseases.

Language: Английский

Citations

46
Comparative Analysis of Core Microbiome Assignments: Implications for Ecological Synthesis DOI Creative Commons
Gordon Custer,

Maya Gans,

Linda T. A. van Diepen

et al.

mSystems, Journal Year: 2023, Volume and Issue: 8(1)

Published: Feb. 6, 2023

The concept of a core microbiome has been broadly used to refer the consistent presence set taxa across multiple samples within given habitat. assignment microbiomes can be performed by several methods based on abundance and occupancy (i.e., detection samples) individual taxa. These approaches have led methodological inconsistencies, with direct implications for ecological interpretation. Here, we reviewed most commonly infer in divergent systems. We applied these using large data sets analyzed simulations determine their accuracy assignments. Our results show that assignments vary significantly types, occupancy-based accurately defining true membership. also found ability capture contingent distribution taxon set. Finally, provide specific recommendations further studies discuss need unifying methodical toward processing advance synthesis. IMPORTANCE Different are assign membership, leading inconsistencies studies. In this study, review compare both simulated empirical data. report inconsistent classifications from methods. Furthermore, demonstrate implication variable may downstream interpretations. Although still lack standardized approach assignments, our study provides direction properly test offers advances model parameterization method choice distinct types.

Language: Английский

Citations

45
Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture DOI Open Access
Weibing Xun, Yunpeng Liu,

Aiyuan Ma

et al.

New Phytologist, Journal Year: 2024, Volume and Issue: 242(6), P. 2401 - 2410

Published: March 17, 2024

Summary The rhizosphere microbiome plays critical roles in plant growth and provides promising solutions for sustainable agriculture. While the frequently fluctuates with soil environment, recent studies have demonstrated that a small proportion of is consistently assembled specific genotype regardless condition, which determined by host genetics. Based on these breakthroughs, involved exploiting plant‐beneficial function microbiome, we propose to divide into environment‐dominated genetic‐dominated components based their different assembly mechanisms. Subsequently, two strategies explore agricultural production are suggested, is, precise management agronomic practices, elucidation genetic basis breeding microbiome‐assisted crop varieties. We finally present major challenges need be overcome implement modulating microbiome.

Language: Английский

Citations

34
A cryptic plasmid is among the most numerous genetic elements in the human gut DOI Creative Commons
Emily C. Fogarty, Matthew S. Schechter, Karen Lolans

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(5), P. 1206 - 1222.e16

Published: Feb. 1, 2024

Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and 14 times as numerous crAssphage, currently established the most abundant element in human gut. The majority of mutations pBI143 accumulate specific positions thousands metagenomes, indicating strong purifying selection. monoclonal individuals, likely due to priority effect version first acquired, from one's mother. can transfer between Bacteroidales, although it does appear impact bacterial host fitness vivo, transiently acquire additional content. important practical applications including its use identifying fecal contamination potential an alternative approach track colonic inflammatory states.

Language: Английский

Citations

30
Current, faltering, and future strategies for advancing microbiome-assisted sustainable agriculture and environmental resilience DOI Creative Commons
Ahmad Humayan Kabir,

Md Zakaria Ibne Baki,

Bulbul Ahmed

et al.

New Crops, Journal Year: 2024, Volume and Issue: 1, P. 100013 - 100013

Published: Jan. 29, 2024

Establishing global sustainable agriculture emerges as the primary, indispensable strategy to meet escalating food demands and address environmental preservation amidst challenges posed by severe climate change. The intricate communities of microorganisms associated with plants, collectively termed plant microbiome, wield significant influence over vitality productivity species. Unleashing potential microbiome stands a pivotal approach safeguard rejuvenate our planet. However, complex nature interactions, coupled their limited persistence in settings due gaps understanding or technological limitations, has impeded substantial progress this field. This review explores innovative revitalized strategies for harnessing microbiome-based enhancements crop fitness. Additionally, we illuminate encountered deciphering interplay between its host, particularly context mitigating adverse influences change on resilience. To navigate these complexities, advocate comprehensive that considers both host microbiome-oriented perspectives. dual-focused aims overcome current limitations pave way toward future where intervention forms bedrock protection.

Language: Английский

Citations

27
A naturally isolated symbiotic bacterium suppresses flavivirus transmission by Aedes mosquitoes DOI
Liming Zhang, Daxi Wang, Peibo Shi

et al.

Science, Journal Year: 2024, Volume and Issue: 384(6693)

Published: April 18, 2024

The commensal microbiota of the mosquito gut plays a complex role in determining vector competence for arboviruses. In this study, we identified bacterium from field Aedes albopictus mosquitoes named Rosenbergiella sp. YN46 ( Rosenbergiella_ YN46) that rendered refractory to infection with dengue and Zika viruses. Inoculation 1.6 × 10 3 colony forming units (CFUs) into A. effectively prevents viral infection. Mechanistically, secretes glucose dehydrogenase Ry GDH), which acidifies lumen fed mosquitoes, causing irreversible conformational changes flavivirus envelope protein prevent entry cells. semifield conditions, exhibits effective transstadial transmission blocks virus by newly emerged adult mosquitoes. prevalence is greater low-dengue areas (52.9 ~91.7%) than those dengue-endemic regions (0 ~6.7%). may offer an safe lead biocontrol.

Language: Английский

Citations

24
Deciphering the core microbes and their interactions in spontaneous Baijiu fermentation: A comprehensive review DOI
Jiamu Kang, Xiaoning Huang, Rengshu Li

et al.

Food Research International, Journal Year: 2024, Volume and Issue: 188, P. 114497 - 114497

Published: May 11, 2024

Language: Английский

Citations

19
Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation DOI Creative Commons
Leonardo Mancabelli, Christian Milani,

Rosita De Biase

et al.

mSystems, Journal Year: 2024, Volume and Issue: 9(4)

Published: March 5, 2024

The human gut microbiota is a dynamic community of microorganisms that undergo variable changes over the entire life span. To thoroughly investigate possible fluctuations throughout life, we performed pooled analysis healthy fecal samples across different age groups covering Our study integrated data from 79 publicly available studies and new stool an Italian cohort, i.e., Parma Microbiota project, resulting in 6,653 processed through shotgun metagenomic approach. This approach has allowed species-level taxonomic reconstruction investigation its metabolic potential From point view, our findings confirmed detailed at accuracy microbial richness gradually increases first stage becoming relatively stable during adolescence. Moreover, identified core representative distinct groups, revealing age-related bacterial patterns continuous rearrangement terms relative abundances span rather than acquisition loss taxa. Furthermore, provided insights into functional contribution microbiome. revealed differences, particularly carbohydrate fiber metabolism, suggesting co-evolution microbiome assembly with diet. Additionally, correlations between vitamin synthesis, such as thiamine niacin, early role physiology, particular functions host's nervous immune systems.

Language: Английский

Citations

18