Single-cell phenotyping and sequencing uncover metabolically active low-abundance yeasts in thermophilic fermentation

#fermentation #metagenomics #phologenetic composition #metabolic activity #Daqu HTD #Pichia kudriavzevii #Wickerhamomyces anomalus #Saccharomycopsis fibuligera #heat-resistance gene #wos2 #FLO8 #single-cell metabolic vitality profile #ecological role 2025-12-16

Tracking production and interconversion of extra- and intra-cellular metabolites during beer fermentation by ramanomics

#beer #Saccharomyces pastorianus #heterogeneity #fermentation monitoring #ramanome #extracellular metabolic phnotypes #alcohol #ester #amino acid #acid #monosaccharide #disaccharide #inter-ramanome correlation analysis #IRCA #process monitoring 2025-12-09

Label-free isolation of lipid-rich Saccharomyces cerevisiae mutant by high-throughput flow-mode Raman-activated cell sorting andmulti-omics analysis for uncovering the mechanism of enhanced lipid accumulation

#palmitoleic acid 2025-07-17

Mining robust in situ phosphorus-accumulating organisms via single-cell RACS-Culture for rational ecosystem engineering

#phosphorus-accumulating organisms (PAO) #Micrococcus luteum #ecosystem engineering 2025-06-14

A pilot study on single-cell Raman spectroscopy combined with machine learning for phenotypic characterization of Staphylococcus aureus

#pathogen identification #phenotypic characterization #Staphylococcus aureus #convolutional neural network #CNN #methicillin-resistant S. aureus #MRSA #rapid bacterial phenotyping 2025-06-08

Label-free high-throughput live-cell sorting of genome-wide random mutagenesis libraries for metabolic traits by Raman flowcytometry

#Raman flow cytometry #DHA #label-free #high-throughput 2025-05-30

Microplastics pose an elevated antimicrobial resistance risk than natural surfaces via a systematic comparative study of surface biofilms in rivers

#microplastics #antimicrobial resistance #AMR #D2O probing #metabolic activity #biofilm 2025-05-26

Raman flow cytometry based single-cell species classification, viable-cell counting and vitality test for probiotic products

#probiotics #quality assessment #viable cell counting #vitality #Raman flow cytometry 2025-05-19

Unraveling antibacterial mechanisms of surfactants against Staphylococcus aureus via single-cell Raman spectroscopy

#antibiotics #antibacterial agents #Staphylococcus aureus #surfactants 2025-04-25

Iron-derepressed robust production of fusarinine C siderophore by Aureobasidium melanogenum

#fermentation #fusarinine C #Aureobasidium melanogenum #Raman flow cytometry 2025-04-23

Detecting and classifying metabolic activity of Staphylococcus aureus by D2O-probed single-cell Raman spectroscopy and machine learning

#pathogen detection #Staphylococcus aureus #D2O probing 2025-03-27

Open-set deep learning-enabled single-cell Raman spectroscopy for rapid identification of airborne pathogens in real-world environments

#airborne pathogen identification #open-set deep learning #high sensitivity #environmental surveillance 2025-01-08

Phylogeny-metabolism dual-directed single-cell genomies for dissecting functional mechanisms of microbiota via FISH-scRACS-Seq

#phylogeny-metabolism dual targeting #microbiota function #P450 2025-01-02

Label-free prediction of tumor metastatic potential via ramanome

#metastatic potential prediction #cancer diagnosis #Ramanome-based metastasis index #machine learning 2024-11-19

Artificial intelligence-assisted automatic Raman-activated cell sorting (AI-RACS) system for mining specific functional microorganisms in the microbiome

#AI #microbiome #in situ functional microorganism #optical tweezers #culture 2024-11-11

Application of Raman spectroscopy and machine learning for Candida auris identification and characterization

#pathogen identification #phenotypic characterization #Candida auris #machine learning #antifugal resistance prediction 2024-10-29

Noninvasive Raman spectroscopy for the detection of rice bacterial leaf blight and bacterial leaf streak

#plant pathogen detection #rice leaves #bacterial infection #early detection #Xanthomonas oryzae #laser tweezers Raman spectroscopy #LTRS 2024-09-24

Rapid antimicrobial susceptibility test of Helicobacter pylori to metronidazole via single-cell Raman spectrometry

#pathogen detection #MIC #Helicobacter pylori #metronidazole resistance #Raman barcodes of cellular-response to stress #drug-resistance mechanism 2024-09-16

Assessing the physiological properties of baker’s yeast based on single-cell Raman spectrum technology

#fermentation #yeast #quality assessment #trehalose #metabolic activity level 2024-09-11

Single-cell exploration of active phosphate solubilizing bacteria across diverse soil matrices for sustainable phosphorus management

#phosphate-solubilizing bacteria (PSB) #low-abundance genera discovery 2024-08-05

Integrating multiple bacterial phenotypes and bayesian network for analyzing health risks of pathogens in plastisphere

#plastisphere #soil microbiome #pathogen abundance #antibiotic resistance gene #ARG #phenotypic resistance to stress #Bayesian network model #health risk 2024-07-01

Aerobic anoxygenic phototrophic bacteria in the marine environments revealed by Raman/fluorescence-guided single-cell sorting and targeted metagenomics

#aerobic anoxygenic phototrophic bacteria #marine environment #culture-independent #16S rRNA gene analysis #metagenome-assembled genome 2024-04-14

Rapid identification of lactic acid bacteria at species/subspecies level via ensemble learning of Ramanomes

#functional lactic acid bacteria #metabolic phenotype detection #ensemble meta-classifier #species/subspecies identification 2024-04-08

Cycloalkane degradation by an uncultivated novel genus of Gammaproteobacteria derived from China’s marginal seas

#uncultivated #Gammaproteobacteria #marine microbiome #methylcyclohexane metabolism 2024-02-28

Culture-free identification of fast-growing cyanobacteria cells by Raman-activated gravity-driven encapsulation and sequencing

#cell factory chassis #carotenoids #cyanobacteria #photosynthetic cell factory 2023-11-11

Rapid Mycobacterium abscessus antimicrobial susceptibility testing based on antibiotic treatment response mapping via Raman microspectroscopy

#rapidly growing mycobacteria #Mycobacterium abscessus #rapid low-cost assay #drug resistance mechanisms 2023-10-30

Impact of airborne pathogen-derived extracellular vesicles on macrophages revealed by Raman spectroscopy and multiomics

#airborne pathogenic bacteria #extracellular vesicles #metabolic alteration #Pseudomonas aeruginosa #proteomic analysis 2023-10-09

Dynamically quantifying intracellular elemental sulfur and predicting pertinent gene transcription by Raman spectroscopy in living cells

#elemental sulfur #Thiophaeococcus mangrovi #mRNA and Raman model #mRR #noninvasive metabolite quantification #gene transcription 2023-06-18

Single cell metabolic phenome and genome via the ramanome technology platform: Precision medicine of infectious diseases at the ultimate precision?

#pathogen detection #single-cell identification, viability and vitality tests and source tracking #D2O probing #metabolic phenome #heterogeneity 2023-05-02

Single-cell rapid identification, in situ viability and vitality profiling, and genome-based source-tracking for probiotics products

#probiotics #quality assessment #Single-Cell Identification, Viability and Vitality tests, and Source-tracking #heterogeneity #D2O probing 2023-04-17

An attempt to simultaneously quantify the polysaccharide, total lipid, protein and pigment in single Cyclotella cryptica cell by Raman spectroscopy

#microalgae #Cyclotella cryptica #polysaccharide, protein and pigment #Intra-ramanome Correlation Analysis 2023-04-08

Robust spontaneous Raman flow cytometry for single-cell metabolic phenome profiling via pDEP-DLD-RFC

#Raman flow cytometry #full-spectrum spontaneous SCRS 2023-03-04

An isotope-labeled single-cell Raman spectroscopy approach for tracking the physiological evolution trajectory of bacteria toward antibiotic resistance

#evolution #antibiotic resistance #D2O probing #evolution trajectory #physiological diversification from isogenic population #genotypic analysis 2023-02-02

Live tracking metabolic networks and physiological responses within microbial assemblages at single-cell level

#live microbial interactions #15N/13C probing #temporal tracking #N and C metabolite exchange 2023-01-18

Identification of pathogens and detection of antibiotic susceptibility at single-cell resolution by Raman spectroscopy combined with machine learning

#pathogen detection #antimicrobial resistance #AMR #machine learning #Acinetobacter baumannii 2023-01-04

Single-cell Raman-activated sorting and cultivation (scRACS-Culture) for assessing and mining in situ phosphate-solubilizing microbes from nature

#phosphate-solubilizing microbes (PSM) #screen-first #scRACS-Culture #scRACS-Seq #uncultured #Cutibacterium spp. 2022-10-30

Revealing CO2-fixing SAR11 bacteria in the ocean by Raman-based single-cell metabolic profiling and genomics

#marine microbiome #seawater #13C-probing #gene #enzyme #Pelagibacter spp. 2022-10-21

Active antibiotic resistome in soils unraveled by single-cell isotope probing and targeted metagenomics

#antibiotic-resistant bacteria #Raman-D2O #metagenomic sequencing #soil active AMR repertoire 2022-09-26

Deep learning-enabled Raman spectroscopic identification of pathogen-derived extracellular vesicles and the biogenesis process

#extracellular vesicle #pathogenic bacterial infection #antimicrobial resistance #AMR #deep learning #attentional neural network #bacterial origin #biogenesis 2022-08-27

Single-cell Raman spectroscopy identifies Escherichia coli persisters and reveals their enhanced metabolic activities

#persister #antibiotic resistance #Escherichia coli #ampicillin #D2O-based single-cell Raman spectroscopy 2022-08-04

Single-cell identification, drug susceptibility test, and whole-genome sequencing of Helicobacter pylori directly from gastric biopsy by clinical antimicrobial susceptibility test Ramanometry

#pathogen detection #MIC #Helicobacter pylori #ID #metabolism inhibition #whole-genome sequencing 2022-06-18

Single-cell Raman microspectroscopy-based assessment of three intracanal disinfectants' effect on Enterococcus faecalis

#pathogen detection #disinfectant assessment #MIC #MIC-MA #Enterococcus faecalis #heterogeneity #quantitative assessment 2022-05-02

Rapid, automated, and reliable antimicrobial susceptibility test from positive blood culture by CAST-R

#pathogen detection #MIC #Acinetobacter baumannii #clinical administration of antimicrobial guidance 2022-04-18

Exploring a blue-light-sensing transcriptional factor to double the peak productivity of oil in Nannochloropsis oceanica

#microalgae #triacylglycerol (TAG) #Nannochloropsis oceanica #stress tolerance #light-sensing transcription factor 2022-03-09

Assessing efficacy of clinical disinfectants for pathogenic fungi by Single-cell Raman Microspectroscopy

#clinical disinfectant efficacy #fungal pathogen #canal-inhabiting microbe #Candida albicans #metabolism-inhibiting #MIC #MIC-MA 2022-02-23

Blood identification at the single-cell level based on a combination of laser tweezers Raman spectroscopy and machine learning

#laser tweezers Raman spectroscopy #LTRS #optical tweezers #substance fingerprint #machine learning algorithm #PCA-LDA #random forest #multi-species blood classification 2021-11-12

Analysis of Raman spectra by using deep learning methods in the identification of marine pathogens

#pathogen identification #long short-term memory neural network #LSTM #CNN #Urechis unicinctus #deep learning 2021-08-02

Novel tigecycline resistance mechanisms in Acinetobacter baumannii mediated by mutations in adeS, rpoB and rrf

#Acinetobacter baumannii #multidrug resistance #tigecycline #resistance mechanism 2021-07-08

Culture-free identification and metabolic profiling of microalgal single cells via ensemble learning of ramanomes

#microalgae #metabolic profiling #culture-independent #resource mining #ramanome database #machine learning 2021-06-18

Genome engineering of Nannochloropsis with hundred-kilobase fragment deletions by Cas9 cleavages

#microalgae #chassis cell #Nannochloropsis oceanica #genome engineering #high growth rate and biomass productivity 2021-05-11

One-cell metabolic phenotyping and sequencing of soil microbiome by Raman-Activated Gravity-driven Encapsulation (RAGE)

#soil microbiome #environmental resource mining #genome #functional cells in complex ecosystems 2021-05-07

Intra-Ramanome Correlation Analysis unveils metabolite conversion network from an isogenic population of cells

#intra-ramanome correlation analysis (IRCA) #metabolic heterogeneity #metabolic conversion network #isogenic propulation 2021-05-01

Microbial metabolism and necromass mediated fertilization effect on soil organic carbon after long-term community incubation in different climates

#soil organic carbon #fertilization effect #D2O probing #soil microbiome #microbial metabolism 2021-03-12

D2O-probed Raman microspectroscopy distinguishes metabolic dynamics of macromolecules in organellar anticancer drug response

#organellar anticancer drug response #metabolic dynamics #multivariate curve resolution #MCF-7 #Saccharomyces cerevisiae #mechanism-bsed screening of drug response 2021-01-12

Phenotypic tracking of antibiotic resistance spread via transformation from environment to clinic by reverse D2O single-cell Raman probing

#antibiotic resistance #transformation #environment #clinic #antibiotic resistance gene #ARG #reverse D2O labeling #Raman-rD2O #spreading risk 2020-11-10

Temporal dynamics of antibiotic resistome in the plastisphere during microbial colonization

#plastisphere #antibiotic resistome #antibiotic resistance gene #ARG #mobile genetic element #MGE #D2O probing 2020-08-19

Positive dielectrophoresis–based Raman-activated droplet sorting for culture-free and label-free screening of enzyme function in vivo

#yeast #triacylglycerol (TAG) #fatty acid degree of unsaturation (FA-DU) #diacylglycerol acyltransferases (DGAT) 2020-08-07

Phenome-genome profiling of single bacterial cell by Raman-Activated Gravity-Driven Encapsulation and Sequencing

#metabolic phenotype profiling #high-coverage single-cell genome sequencing #microdroplet #Escherichia coli 2020-06-09

Combination of an artificial intelligence approach and laser tweezers Raman spectroscopy for microbial identification

#microbe identification #convolutional neural network #ConvNet #CNN #Raman feature weight visualization 2020-04-13

Classification of pathogens by Raman spectroscopy combined with generative adversarial networks

#pathogen identification #marine ecology #marine pathogen #Staphylococcus hominis #Vibrio alginolyticus #Bacillus licheniformis #generative adversarial network #GAN #machine learning classification #potential identifying region 2020-04-04

Raman-activated cell sorting and metagenomic sequencing revealing carbon-fixing bacteria in the ocean

#marine microbiome #Synechococcus spp. #Pelagibacter spp. #13C probing #metagenomic sequencing 2018-06-01

Raman-Activated Droplet Sorting (RADS) for label-free high-throughput screening of microalgal single-cells

#functional screening #microalgae #Haematococcus pluvialis #AXT #sequencing #cultivation 2017-11-21

Label-free, simultaneous quantification of starch, protein and triacylglycerol in single microalgal cells by Ramanome

#microalgae #triacylglycerol (TAG) #strain screening #bioprocess control 2017-11-11

Metabolic-activity-based assessment of antimicrobial effects by D2O-labeled single-cell Raman microspectroscopy

#MIC #MIC-MA #heterogeneity index #D2O-Raman #nongrowing but metabolically active #quantitative #metabolic activity 2017-03-10

Label-free, rapid and quantitative phenotyping of stress response in E. coli via ramanome

#stress response phenotyping #Escherichia coli #mechanism-specific #heterogeneity 2016-10-19

Reverse and multiple stable isotope probing to study bacterial metabolism and interactions at the single cell level

#microorganism interactions #D2O probing #Acinetobacter baylyi #Escherichia coli #metabolic activity 2016-10-04

Raman-activated cell sorting based on dielectrophoretic single-cell trap and release

#information-rich #carotenoid #Saccharomyces cerevisiae 2015-02-17

Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells

#microbial activity measurement #D2O probing #Escherichia coli #Akkermansia muciniphila #Bacteroides acidifaciens #optical tweezers 2015-01-13

Raman spectroscopy provides a rapid, non-invasive method for quantitation of starch in live, unicellular microalgae

#microalgae #starch #Chlamydomonas reinhardtii #Chlorella pyrenoidosa #ADP-glucose pyrophosphorylase 2014-12-01

Quantitative dynamics of triacylglycerol accumulation in microalgae populations at single-cell resolution revealed by Raman microspectroscopy

#microalgae #triacylglycerol (TAG) #Nannochloropsis oceanica #biofuel 2014-04-09

Raman activated cell ejection for isolation of single cells

#oral microbiome #13C/15N probing #bacterial type classification 2013-11-19