Microbiome single cell atlases generated with a commercial instrument DOI Creative Commons
Adam R. Abate, Xiangpeng Li, Linfeng Xu

et al.

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 14, 2023

Single cell sequencing is useful for resolving complex systems into their composite types and computationally mining them unique features that are masked in pooled sequencing. However, while commercial instruments have made single analysis widespread mammalian cells, analogous tools microbes limited. Here, we present EASi-seq (Easily Accessible microbe sequencing). By adapting the workflow of Mission Bio Tapestri instrument, this method allows efficient individual microbes' genomes. thousands to be sequenced per run and, as show, can generate detailed atlases human environmental microbiomes. The ability capture large shotgun genome datasets from provides new opportunities discovering analyzing species subpopulations. To facilitate this, develop a companion bioinformatic pipeline clusters by similarity, improving whole assembly, strain identification, taxonomic classification, gene annotation. In addition, demonstrate integration metagenomic contigs with reduce bias increase coverage. Overall, enables high quality genomic data microbiome samples using an accessible on commercially available platform.

Language: Английский

Advancing marine cellulose-based packaging: A review on sustainable biorefinery perspectives DOI
P. Senthilkumar,

Bernadette Kumar,

Gunalan Sivakumar

et al.

Biomass and Bioenergy, Journal Year: 2025, Volume and Issue: 197, P. 107849 - 107849

Published: April 6, 2025

Language: Английский

Citations

0
Microbiome engineering to palliate microbial dysbiosis occurring in agroecosystems DOI
Romain Darriaut, Céline Roose‐Amsaleg, Mathieu Vanhove

et al.

Microbiological Research, Journal Year: 2025, Volume and Issue: unknown, P. 128178 - 128178

Published: April 1, 2025

Language: Английский

Citations

0
Soil microbiome characterization and its future directions with biosensing DOI Creative Commons

Lexi DeFord,

Jeong‐Yeol Yoon

Journal of Biological Engineering, Journal Year: 2024, Volume and Issue: 18(1)

Published: Sept. 10, 2024

Language: Английский

Citations

3
Main Manuscript for Microbiome single cell atlases generated with a benchtop instrument DOI Open Access
Xiangpeng Li, Linfeng Xu, Benjamin Demaree

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 10, 2023

Single cell sequencing is useful for resolving complex systems into their composite types and computationally mining them unique features that are masked in pooled sequencing. However, while commercial instruments have made single analysis widespread mammalian cells, analogous tools microbes limited. Here, we present EASi-seq (Easily Accessible microbe sequencing). By adapting the workflow of Mission Bio Tapestri instrument, this method allows efficient individual microbes' genomes. thousands to be sequenced per run and, as show, can generate detailed atlases human environmental microbiomes. The ability capture large shotgun genome datasets from provides new opportunities discovering analyzing species subpopulations. To facilitate this, develop a companion bioinformatic pipeline clusters by similarity, improving whole assembly, strain identification, taxonomic classification, gene annotation. In addition, demonstrate integration metagenomic contigs with reduce bias increase coverage. Overall, enables high quality genomic data microbiome samples using an accessible on commercially available platform.

Language: Английский

Citations

7
Nature AND Nurture: Enabling formate-dependent growth inMethanosarcina acetivorans DOI Creative Commons
Jichen Bao, Tejas Somvanshi,

Yufang Tian

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 9, 2024

Abstract Methanogenic archaea are crucial in global carbon cycling as around 1 Gt of the potent greenhouse gas, methane, is produced annually. Major contributors belong to order Methanosarcinales, which contain some most versatile methanogens that capable acetotrophic, methylotrophic and CO 2 -reducing methanogenesis. The genetically tractable model methanogen, Methanosarcina acetivorans , by its nature shows versatility substrate utilization energy conservation pathways but cannot utilize formate. In this study, we expanded primary metabolism M. include formate-dependent By introducing an exogenous formate dehydrogenase, two metabolically engineered strains acquired capacity for methanogenesis with one methyl-reduction other -reduction. Through nurturing strain -reduction adaptive laboratory evolution, were able enable growth solely on formate, a only reported without cytochromes limited their versatility. also showed acetogenic potential where was divert ≈ 10% acetate instead methane. Our results show even though lacks converting hydrogenase use H it has yet-uncharacterized obtain reduced ferredoxins from oxidizing work encourages reevaluation our understanding Methanosarcinales. enabling methanogenesis, have spectrum methanogen well.

Language: Английский

Citations

2
Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications DOI Creative Commons

I. C. Cunha-Ferreira,

Carla Simone Vizzotto, Tayná Diniz Frederico

et al.

Engineering Microbiology, Journal Year: 2024, Volume and Issue: 4(3), P. 100163 - 100163

Published: July 22, 2024

The biotechnological industry faces a crucial demand for novel bioactive compounds, particularly antimicrobial agents, to address the rising challenge of bacterial resistance current available antibiotics. Traditional strategies cultivating naturally occurring microorganisms often limit discovery producers. This study presents protocol targeted selection strains using supernatant

Language: Английский

Citations

2
Culturomics- and metagenomics-based insights into the soil microbiome preservation and application for sustainable agriculture DOI Creative Commons
Elisa Clagnan, Manuela Costanzo, Andrea Visca

et al.

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: Oct. 24, 2024

Soil health is crucial for global food production in the context of an ever-growing population. Microbiomes, a combination microorganisms and their activities, play pivotal role by biodegrading contaminants, maintaining soil structure, controlling nutrients' cycles, regulating plant responses to biotic abiotic stresses. Microbiome-based solutions along soil-plant continuum, scaling up from laboratory experiments field applications, hold promise enhancing agricultural sustainability harnessing power microbial consortia. Synthetic communities, i.e., selected consortia, are designed perform specific functions. In contrast, natural communities leverage indigenous populations that adapted local conditions, promoting ecosystem resilience, reducing reliance on external inputs. The identification indicators requires holistic approach. It fundamental current understanding status providing comprehensive assessment sustainable land management practices conservation efforts. Recent advancements molecular technologies, such as high-throughput sequencing, revealed incredible diversity microbiomes. On one hand, metagenomic sequencing allows characterization entire genetic composition microbiomes, examination functional potential ecological roles; other culturomics-based approaches metabolic fingerprinting offer complementary information snapshots activities both

Language: Английский

Citations

2
Approaches for attaining clean bacterial fractions from complex environmental samples DOI Creative Commons
Jaeyoung Yu,

Marika Kawahisa,

Aya Kinoshita

et al.

Frontiers in Marine Science, Journal Year: 2024, Volume and Issue: 11

Published: March 27, 2024

Marine bacteria have been targeted by industry and pharmaceutics as genetic resources for highly active enzymes or novel lead compounds. Although numerous techniques introduced to isolate useful from the environment, we are still dependent on conventional direct cultivation method attain pure cultures. However, efficient bacterial isolation is hindered several factors, including presence of impurities. In this work, demonstrate significance removing impurities their impact isolation, employed two approaches: dielectrophoresis (DEP) fluorescent D-amino acids (FDAA). We successfully attained clean fractions applicable downstream processing using these approaches, uniquely designed identify based characteristics features. The diversity both approaches was investigated 16S rRNA sequencing compared that standard differential centrifugation method. addition, viability isolates also determined via cultivation. As a result, separation allowed identification unique each approach. Successful suggested were attaining viable bacteria. conclusion, promotes thus could aid in successful within complex environmental samples.

Language: Английский

Citations

1
Elasmobranchs Exhibit Species-Specific Epidermal Microbiomes Guided by Denticle Topography DOI Creative Commons
Asha Z. Goodman, Bhavya Papudeshi, María F. Mora

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 6, 2024

Abstract Elasmobranch epidermal microbiomes are species-specific, yet microbial assembly and retainment drivers mainly unknown. The contribution of host-derived factors in recruiting an associated microbiome is essential for understanding host-microbe interactions. Here, we focus on the physical aspect host skin structuring communities. Each species elasmobranch exhibits unique denticle morphology, investigate whether communities functional pathways correlated with morphological features or follow phylogeny three species. We extracted sequenced DNA from captive shark species: Horn ( Heterodontus francisci ), Leopard Triakis semifasciata Swell Cephaloscyllium ventriosum ) use electron microscopy to measure dermal each Our results outline species-specific communities, as compositions vary at phyla level; C. hosted a higher relative abundance Pseudomonadota Bacillota, while H. were prevalence Euryarchaeota Aquificae, Bacteroidota Crenarchaeota ubiquitous T. . Functional performed by species’ respective metabolic. Microbial genes aminosugars electron-accepting reactions distance between denticles, whereas desiccation stress only present when overlapped. Pyrimidines, chemotaxis virulence followed sharks. Several genera display associations that resemble evolutionary lineage, others had linear relationships interdenticle distance. Therefore, morphology was selective influence some microbes functions contributing phylosymbiosis. Importance form vertebrate hosts, but these remain outstanding question. explore relationship feature community. A distinguishing subclass Elasmobranchii (sharks, rays, skates), presence denticles skin. These structures protrude through epidermis providing increased swimming efficiency artificial model affect recruitment establishment cultured has not been tested natural microbiomes. show naturally occurring attributes features, suggesting they one, factor structure benthic

Language: Английский

Citations

1
Quorum Sensing Regulates Virulence Factors in the Coral Pathogen Vibrio coralliilyticus DOI Open Access
Victoria N. Lydick,

Shir Mass,

Robert Pepin

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 10, 2024

ABSTRACT The bacterial pathogen Vibrio coralliilyticus ( Vcor ) causes disease in coral species worldwide. mechanisms of colonization, microbiome interactions, and virulence factor production are understudied. In other model species, factors like biofilm formation, toxin secretion, protease controlled through a density-dependent communication system called quorum sensing (QS). Comparative genomics indicated that V. genomes share high sequence identity for most the QS signaling regulatory components identified species. Here, we identify an active pathway two strains with distinct infection etiologies: type strain BAA-450 isolate OCN008. inter-species AI-2 autoinducer both controls expression master transcription VcpR to regulate >300 genes, including production, conserved VI secretion systems (T6SSs). Activation T6SS1 by results effectors enables interbacterial competition killing prey bacteria. We conclude is functional genes involved relevant behaviors may influence infection. IMPORTANCE infects many marine organisms, multiple corals, primary causative agent tissue loss diseases bacterial-induced bleaching. Here investigate common cell-cell mechanism sensing, which known be intimately connected Our genetic chemical studies uncovered directly regulates key factors: proteases, biofilms, systems. These findings connect communities lead novel treatments earlier diagnoses reefs.

Language: Английский

Citations

1