[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"$fxLN3MUwXCdr5RPjwZYIDpOj8CHyjOmngWTgoKXPtZbg":3,"$ffBWZEPS6EPgqva4zgZEFf1tOC8ywrLEKoyM0sQq6TgQ":36,"$f3Ft0rKFJHppdzE-vuveecxx1BUcg9iOlMLtyzf_MJDg":102,"$fucxFBm2ZjZfGSdmdRaSNGBI_F0jJme4f0GTvzUhQfL8":166},[4,8,12,16,20,24,28,32],{"title":5,"slug":6,"path":7},"About Microbeonline.com","about-microbeonline-com","\u002Fabout-microbeonline-com\u002F",{"title":9,"slug":10,"path":11},"About Me","about-me","\u002Fabout-microbeonline-com\u002Fabout-me\u002F",{"title":13,"slug":14,"path":15},"Advertise with Us","advertise-us","\u002Fadvertise-us\u002F",{"title":17,"slug":18,"path":19},"Privacy Policy","privacy-policy","\u002Fprivacy-policy\u002F",{"title":21,"slug":22,"path":23},"Abbreviations","abbreviations","\u002Fabbreviations\u002F",{"title":25,"slug":26,"path":27},"Microbes","microbes","\u002Fmicrobes\u002F",{"title":29,"slug":30,"path":31},"Books","recommended-books","\u002Frecommended-books\u002F",{"title":33,"slug":34,"path":35},"Utilization Tests for Bacterial Identification","utilization-tests","\u002Futilization-tests\u002F",{"type":37,"data":38},"blog",{"slug":39,"title":40,"description":41,"seoTitle":42,"seoDescription":42,"author":43,"createdDate":44,"lastUpdatedDate":44,"draft":45,"category":46,"image":42,"body":47,"faq":48,"commentsClosed":45,"tags":70,"related":71,"comments":98},"dna-microarray-principle-procedure-types","DNA Microarray: Principle, Procedure, Types, and How to Read the Results","How a DNA microarray measures the activity of thousands of genes at once by hybridization, how the two-color comparison works, how to read red, green, and yellow spots, the main types of microarray, and its uses and limitations.",null,"Acharya Tankeshwar","2026-08-01",false,"molecular-biology","A single glass slide the size of a thumbnail can carry more than twenty thousand tiny DNA spots, one for almost every gene in the human genome. Wash a labeled sample across it, and each spot lights up in proportion to how active its gene was in that sample. In one experiment, you read the behavior of the entire genome at once. That is the idea behind the DNA microarray: instead of asking about one gene at a time, you ask about all of them together, and let each gene report itself by finding its matching partner on the chip.\n\n## What a DNA microarray is\n\nA DNA microarray (also called a DNA chip or gene chip) is a slide or chip carrying thousands of microscopic spots arranged in a grid. Each spot holds many copies of a known, single-stranded DNA sequence called a probe, and each probe corresponds to a specific gene or DNA sequence. When labeled DNA from a sample is applied to the chip, it binds only to the spots whose probes it matches, a process called hybridization. Measuring how much sample bound at each spot tells you how much of that sequence was present in the sample.\n\nThe microarray is the chip and the assay. The instrument that reads it, exciting the fluorescent labels and measuring the light from each spot, is a separate device, the microarray scanner, covered in detail in [our article on the microarray scanner](https:\u002F\u002Fmicrobeonline.com\u002Fmicroarray-scanner-principle-and-parts\u002F). This article focuses on the microarray itself: how it works, its types, and how to interpret the result.\n\n## The principle: hybridization\n\nThe entire technique rests on one property of DNA: complementary base pairing. A single strand of DNA will bind specifically to another single strand carrying the complementary sequence, A with T, G with C, forming a stable double strand held by hydrogen bonds. This specific binding is called nucleic acid hybridization.\n\nOn a microarray, the probes are single-stranded and anchored to the chip. When single-stranded sample DNA (or DNA made from the sample's RNA) is washed over the chip, each sample fragment binds only to the spot whose probe is its complement. A fragment with no matching probe washes away. Because each spot's sequence is known in advance, the position of a bound, glowing spot tells you which gene it represents, and the brightness tells you how much bound.\n\n## The two-color comparison: reading the spots\n\nMost classic expression microarrays are run as a two-color comparison, and understanding this design is the key to reading the result.\n\n\u003Cfigure>\n\u003Cimg src=\"https:\u002F\u002Fassets.microbeonline.com\u002Fblogs\u002Ftwo-color-microarray-workflow.png\" alt=\"Two-color DNA microarray workflow: sample A labeled with Cy3 green dye and sample B with Cy5 red dye are mixed, hybridized to one chip, washed, and scanned to give a red-to-green ratio for each gene.\" width=\"2720\" height=\"1360\" draggable=\"false\" contenteditable=\"false\">\u003Cfigcaption>Figure 1. The two-color microarray workflow. Two samples are labeled with different fluorescent dyes (Cy3 green and Cy5 red), mixed, and hybridized to the same chip, where they compete to bind each spot. One chip compares both samples across thousands of genes at once.\u003C\u002Ffigcaption>\n\u003C\u002Ffigure>\n\n**Setting up the comparison.** Two samples are compared on one chip, for example, healthy tissue versus tumor tissue, or untreated versus treated cells. RNA is extracted from each, converted to complementary DNA (cDNA), and each sample's cDNA is labeled with a different fluorescent dye: one sample with Cy3 (which fluoresces green) and the other with Cy5 (which fluoresces red). The two labeled samples are mixed and hybridized together to the same chip, so at every spot the two samples compete to bind their shared probe.\n\n**Reading the spots.** After washing off unbound cDNA, the scanner measures green and red fluorescence at each spot, and the color of the spot tells you which sample expressed that gene more:\n\n\u003Cfigure>\n\u003Cimg src=\"https:\u002F\u002Fassets.microbeonline.com\u002Fblogs\u002Freading-microarray-spot-colors.png\" alt=\"DNA microarray spot color key: a red spot means the gene was more active in the Cy5-labeled sample, green means more active in the Cy3-labeled sample, yellow means equal expression in both, and a dark spot means neither sample expressed the gene.\" width=\"2720\" height=\"1200\" draggable=\"false\" contenteditable=\"false\">\u003Cfigcaption>Figure 2. Reading microarray spot colors. The color points back to which sample expressed the gene more, not to the gene itself. Yellow indicates equal expression in both samples, not a separate type of gene.\u003C\u002Ffigcaption>\n\u003C\u002Ffigure>\n\nA red spot means the gene was more active in the Cy5-labeled sample. More red-labeled cDNA bound, so that sample had more of this transcript.\n\nA green spot means the gene was more active in the Cy3-labeled sample.\n\nA yellow spot means both samples expressed the gene about equally. Roughly equal red and green combine to yellow.\n\nA black or dark spot means neither sample expressed the gene; almost nothing bound.\n\nThe numerical version of this is the red-to-green intensity ratio at each spot, which quantifies how much more active a gene was in one sample than the other. Reading a microarray, then, is reading a field of colored spots as a genome-wide comparison of two conditions.\n\n## Procedure\n\nThe workflow from sample to data has four stages.\n\n**1. Chip preparation.** The probes are attached to the chip in an ordered grid. Two main manufacturing approaches are used. In situ synthesis builds the probes base by base directly on the chip surface using photolithography and light-directed chemistry (the approach used for high-density oligonucleotide arrays). Spotted arrays instead take pre-made probes and deposit them onto the chip with a robotic printer. Many chips are now bought commercially ready-made.\n\n**2. Sample preparation and labeling.** RNA is extracted from each sample, then converted to more stable complementary DNA (cDNA). During this step a fluorescent dye is incorporated, Cy3 or Cy5 for a two-color experiment. (Single-color platforms label one sample per chip and compare across chips instead.)\n\n**3. Hybridization.** The labeled sample is applied to the chip and incubated, allowing fragments to find and bind their complementary probes. The chip is then washed to remove unbound and loosely bound material, leaving only specifically hybridized sample.\n\n**4. Scanning and analysis.** The [microarray scanner](https:\u002F\u002Fmicrobeonline.com\u002Fmicroarray-scanner-principle-and-parts\u002F) excites the dyes, measures the fluorescence at each spot, and produces a digital image. Software converts each spot to an intensity value, subtracts local background, and (in two-color experiments) computes the red-to-green ratio, turning the image into a table of expression values gene by gene.\n\n## Types of microarray\n\nAlthough gene-expression arrays are the most familiar, the same hybridization principle is used for several distinct purposes.\n\n\u003Cfigure>\n\u003Cimg src=\"https:\u002F\u002Fassets.microbeonline.com\u002Fblogs\u002Fmicroarray-hybridization-principle.png\" alt=\"Hybridization on a microarray spot: a single-stranded probe anchored to the chip binds complementary sample DNA through base pairing, producing a fluorescent signal, while non-matching sample DNA fails to bind and washes away.\" width=\"2720\" height=\"1440\" draggable=\"false\" contenteditable=\"false\">\u003Cfigcaption>Figure 3. The hybridization principle. Each spot carries a known single-stranded probe. Sample DNA binds only where its sequence is complementary to the probe, so a spot glows only if the sample carries that matching sequence. Non-matching fragments wash away.\u003C\u002Ffigcaption>\n\u003C\u002Ffigure>\n\n**Expression microarrays** measure how actively genes are transcribed, by hybridizing labeled cDNA made from a sample's RNA. This is the two-color comparison described above, used to compare gene activity between conditions such as diseased and healthy tissue.\n\n**Genotyping microarrays (SNP arrays)** detect single-nucleotide polymorphisms, single-base differences in the genome, rather than expression. The probes are designed so that a sample's DNA binds differently depending on which base it carries at a given position, allowing thousands to millions of genetic variants to be typed at once. These are used in genome-wide association studies and in clinical genetic testing.\n\n**Comparative genomic hybridization (CGH) arrays** detect gains and losses of DNA (copy-number changes) rather than expression or single bases. Sample and reference DNA are labeled with two dyes and co-hybridized, and the ratio at each spot reveals whether a region is duplicated or deleted in the sample. Array CGH is widely used to find chromosomal imbalances in cancer and in constitutional disorders.\n\nThe common thread across all three: known probes on a chip, labeled sample DNA, and hybridization read out as fluorescence. What changes is what the probes are designed to detect.\n\n## Uses of DNA microarray\n\nMicroarrays are used wherever many sequences must be measured in parallel. In gene-expression profiling, they compare which genes are active between conditions, for example, identifying genes switched on in a tumor versus normal tissue. In cancer classification, expression patterns help distinguish tumor subtypes that look similar under the microscope but behave differently, informing prognosis and treatment choice. In pharmacogenomics and drug research, they reveal how cells respond to a drug at the level of gene activity. In genetic testing and research, SNP and CGH arrays detect variants and copy-number changes linked to disease. In microbiology, arrays can be designed to detect and identify pathogens or resistance genes by their sequences.\n\n## Limitations of DNA microarray\n\n**It measures what you put on the chip.** A microarray can only detect sequences for which probes were designed. Genes or variants not represented by a probe are invisible to it. This is a key difference from RNA sequencing, which can detect transcripts without prior knowledge of their sequence.\n\n**Relative, not absolute, quantification.** A microarray measures fluorescence intensity, which is quantitative, but it usually reports relative expression, how much more active a gene is in one sample than another, rather than an absolute transcript count. Results are often confirmed with quantitative PCR.\n\n**It measures transcripts, not proteins.** Expression arrays report mRNA levels. They cannot capture what happens after transcription, so a gene that is transcribed but not translated into protein, or a protein regulated after it is made, will not be reflected. Microarray data describes transcription, not the final protein output.\n\n**Reproducibility and cross-hybridization.** Signal can vary between runs, and closely related sequences can bind the wrong probe (cross-hybridization), adding noise. Careful normalization and validation are needed.\n\n## How to Remember\n\n**The chip binds, the scanner reads.** The microarray does the biology, probes catching complementary sample DNA by hybridization. The scanner does the physics, exciting dyes and measuring light. Keep the two jobs apart and the topic gets simpler.\n\n**Red, green, yellow: who won the spot.** Two samples compete at each spot. Red means the red-labeled sample expressed that gene more, green means the green-labeled sample did, yellow means a tie, black means neither. The color is a scoreboard for each gene. To keep the dyes straight: Cy3 is green, Cy5 is red, so the lower number is the cooler color.\n\n**Hybridization is just A-T, G-C, at scale.** The whole technique is complementary base pairing repeated across thousands of spots. Every spot is one small hybridization experiment, and the chip runs them all at once.\n\n**Probes are chosen in advance, so you only see what you look for.** A microarray answers questions you designed probes for. Anything without a probe is invisible. That one fact explains its biggest limitation and how it differs from sequencing.\n\n## Key exam facts in one table\n\n| Concept | Fact to remember |\n| --- | --- |\n| Core principle | Nucleic acid hybridization: single-stranded sample DNA binds complementary probes fixed on the chip |\n| What a probe is | A known single-stranded DNA sequence anchored to a spot, one gene or sequence per spot |\n| Two-color labeling | Cy3 (green) and Cy5 (red) label two samples hybridized together on one chip |\n| Reading spots | Red = higher in Cy5 sample; green = higher in Cy3 sample; yellow = equal; black = neither |\n| Quantification | Fluorescence intensity is quantitative but usually reported as a relative ratio, not absolute counts |\n| Expression array | Measures gene activity from labeled cDNA (made from RNA) |\n| SNP (genotyping) array | Detects single-base variants across the genome |\n| CGH array | Detects copy-number gains and losses by comparing sample and reference DNA |\n| Key limitation | Only detects sequences with probes on the chip; measures mRNA, not protein |\n| Reads the chip | The microarray scanner (a separate instrument) excites the dyes and digitizes the signal |\n\n## Where Students Get Confused\n\n**The microarray is not the scanner.** The microarray is the chip and the assay. The scanner is the instrument that reads it. They are different things, and this article is about the chip.\n\n**Which color means what.** In a two-color experiment, a red spot means the gene was more active in the sample labeled with the red dye (Cy5), and green means more active in the Cy3 sample. Yellow is equal expression, not a separate gene state. Students often forget the color points back to which sample, not to the gene itself.\n\n**Hybridization happens before scanning.** By the time a chip is scanned, sample has already bound to probes and the chip has been washed. Scanning only measures the result; it does not cause the binding.\n\n**Probes are known; samples are unknown.** The sequence at each spot is designed in advance. What you are measuring is how much of the unknown sample binds there. The chip is the reference; the sample is the question.\n\n**Microarray versus RNA-seq.** A microarray only detects sequences it has probes for. RNA sequencing reads whatever transcripts are present without needing probes designed first. This is why sequencing has largely overtaken microarrays for discovery, though arrays remain useful for targeted, standardized testing.\n\n**Expression, SNP, and CGH arrays are not the same.** All use hybridization, but they detect different things: gene activity, single-base variants, and copy-number changes, respectively. The word microarray alone does not tell you which.\n\n**References**\n\n1. Brown TA. *Genomes 5.* 5th ed. Boca Raton: CRC Press; 2023.\n2. Buckingham L. *Molecular Diagnostics: Fundamentals, Methods, and Clinical Applications.* 4th ed. Philadelphia: F.A. Davis; 2026.\n3. Wiltgen M, Tilz G. DNA microarray analysis: principles and clinical impact. *Hematology.* 2007;12(4):271-287. doi:10.1080\u002F10245330701283967\n4. National Human Genome Research Institute. DNA Microarray Technology Fact Sheet. [genome.gov](http:\u002F\u002Fgenome.gov); 2020. Available at: \u003Chttps:\u002F\u002Fwww.genome.gov\u002Fabout-genomics\u002Ffact-sheets\u002FDNA-Microarray-Technology>",[49,52,55,58,61,64,67],{"question":50,"answer":51},"\u003Cp>What is the principle of a DNA microarray?\u003C\u002Fp>","\u003Cp>It is nucleic acid hybridization. Each spot on the chip holds a known single-stranded DNA probe. Labeled single-stranded sample DNA is washed over the chip and binds only to the spots with complementary sequences. Measuring the fluorescence at each spot shows how much of that sequence was in the sample.\u003C\u002Fp>",{"question":53,"answer":54},"\u003Cp>What do the colors on a microarray mean?\u003C\u002Fp>","\u003Cp>In a two-color experiment, two samples are labeled with different dyes, green (Cy3) and red (Cy5), and hybridized to the same chip. A red spot means the gene was more active in the red-labeled sample, green means more active in the green-labeled sample, yellow means both expressed it about equally, and a dark spot means neither expressed it.\u003C\u002Fp>",{"question":56,"answer":57},"\u003Cp>What is the difference between a DNA microarray and a microarray scanner?\u003C\u002Fp>","\u003Cp>The DNA microarray is the chip carrying the probes and the hybridized sample, it is where the biology happens. The microarray scanner is the separate instrument that excites the fluorescent dyes and measures the light from each spot to produce data.\u003C\u002Fp>",{"question":59,"answer":60},"\u003Cp>What is the difference between expression, SNP, and CGH microarrays?\u003C\u002Fp>","\u003Cp>Expression arrays measure how actively genes are transcribed, using labeled cDNA made from RNA. SNP (genotyping) arrays detect single-base genetic variants. CGH arrays detect gains and losses of DNA (copy-number changes) by comparing sample and reference DNA. All three use hybridization but answer different questions.\u003C\u002Fp>",{"question":62,"answer":63},"\u003Cp>Is microarray data quantitative?\u003C\u002Fp>","\u003Cp>Yes, but usually relative. The measured fluorescence intensity is a quantitative signal, but microarray experiments typically report how much more active a gene is in one sample than another (a ratio) rather than absolute transcript numbers. Results are often validated by quantitative PCR.\u003C\u002Fp>",{"question":65,"answer":66},"\u003Cp>Why has RNA sequencing largely replaced microarrays?\u003C\u002Fp>","\u003Cp>A microarray can only detect sequences it has probes for, so it cannot discover unknown transcripts. RNA sequencing reads whatever is present without needing probes designed in advance, giving broader coverage and a wider quantitative range. Microarrays remain useful for standardized, targeted, lower-cost testing.\u003C\u002Fp>",{"question":68,"answer":69},"\u003Cp>Can microarrays be used in microbiology?\u003C\u002Fp>","\u003Cp>Yes. Arrays can be designed with probes for pathogen sequences or resistance genes, allowing many organisms or genetic markers to be detected and identified in parallel from one sample.\u003C\u002Fp>",[],[72],{"slug":73,"title":74,"description":75,"seoTitle":42,"seoDescription":42,"author":76,"createdDate":77,"lastUpdatedDate":44,"draft":45,"category":78,"image":42,"faq":79,"tags":97},"microarray-scanner-principle-and-parts","Microarray Scanner: How It Detects Fluorescence, PMT vs. CCD, Parts, and How to Choose One","How a microarray scanner detects fluorescent signal from a hybridized DNA chip, the difference between PMT laser scanners and CCD camera imagers, the parts of a scanner, and how to choose one for your laboratory.","Ashma Shrestha","2022-06-30","lab-equipment",[80,83,86,89,92,95],{"question":81,"answer":82},"\u003Cp>What does a microarray scanner do?\u003C\u002Fp>","\u003Cp>It reads a hybridized DNA microarray. The scanner shines laser light on the chip to excite the fluorescent dyes bound at each spot, measures the light each spot emits, and converts those measurements into a digital image and numerical intensity values that show how much labeled sample bound at each spot.\u003C\u002Fp>",{"question":84,"answer":85},"\u003Cp>What is the difference between a PMT scanner and a CCD imager?\u003C\u002Fp>","\u003Cp>A PMT (photomultiplier tube) scanner uses a focused laser that scans the chip point by point with confocal optics, giving high sensitivity and a wide dynamic range but slower scans. A CCD imager illuminates a whole area at once and captures it with a camera sensor, which is faster and simpler but usually has a narrower dynamic range.\u003C\u002Fp>",{"question":87,"answer":88},"\u003Cp>What are Cy3 and Cy5 in microarray scanning?\u003C\u002Fp>","\u003Cp>They are two fluorescent dyes commonly used to label samples. Cy3 fluoresces green and Cy5 fluoresces red. In a two-color experiment, two samples are labeled with the two dyes, hybridized to the same chip, and the scanner measures the red-to-green ratio at each spot to compare the samples.\u003C\u002Fp>",{"question":90,"answer":91},"\u003Cp>Does the scanner perform the hybridization?\u003C\u002Fp>","\u003Cp>No. Hybridization, where labeled sample DNA binds to complementary probes on the chip, happens before scanning. The chip is then washed to remove unbound sample. The scanner only measures the fluorescence remaining at each spot.\u003C\u002Fp>",{"question":93,"answer":94},"\u003Cp>Why does a microarray scanner need optical filters?\u003C\u002Fp>","\u003Cp>Because each dye emits light at a longer wavelength than the light used to excite it. Filters let the weaker emitted fluorescence through to the detector while blocking the much stronger reflected excitation light, so the detector measures only the signal from the dye.\u003C\u002Fp>",{"question":62,"answer":96},"\u003Cp>Yes, but usually in a relative sense. The scanner measures fluorescence intensity, which is a quantitative signal, but microarray experiments typically report relative expression (such as a ratio between two samples) rather than absolute transcript counts, and results are often confirmed with qPCR.\u003C\u002Fp>",[],{"enabled":99,"threads":100,"total":101},true,[],0,[103,109,115,122,128,133,139,144,150,153,160],{"slug":104,"name":43,"description":105,"image":106,"body":107,"postCount":108},"acharya-tankeshwar","Editor-in-chief","https:\u002F\u002Fassets.microbeonline.com\u002Fauthors\u002Ftankeshwar-acharya-author-microbeonline.jpg","***Tankeshwar Acharya, MSc (Medical Microbiology)***\n\n*Tankeshwar Acharya is an Assistant Professor in the Department of Microbiology at Patan Academy of Health Sciences (PAHS), Nepal, where he has been teaching and practicing clinical microbiology for over 14 years. He is the founder of Microbe Online, one of the leading free microbiology education resources on the web, covering bacteriology, mycology, parasitology, immunology, and clinical laboratory diagnostics written from direct experience in both the classroom and the diagnostic laboratory.*",468,{"slug":110,"name":76,"description":111,"image":112,"body":113,"postCount":114},"ashma-shrestha","SEO Copywriter and Science Communicator\nKathmandu, Nepal","https:\u002F\u002Fassets.microbeonline.com\u002Fauthors\u002Fashma-shrestha.png","Ashma Shrestha holds a Master of Science in Medical Microbiology from the Institute of Science and Technology (IOST), Tribhuvan University, Nepal, where she developed a strong foundation in virology, molecular biology, and diagnostic microbiology.\n\nShe now works as an SEO Copywriter at Resolution Digital, where she combines her scientific training with research-driven content strategy. She is certified in Google Analytics and Google Business Profile (GBP), and brings a data-informed approach to science communication writing content that is not only accurate but structured to reach and serve the students who need it most.\n\nAt microbeonline, Ashma contributes articles primarily in virology and molecular biology, areas she finds most compelling for their mechanistic depth and their growing clinical relevance. Her writing reflects the same standard the site is built on: factual rigor, clear explanation of the *why* behind microbiology concepts, and content that helps students move from memorization to genuine understanding.\n\nShe is passionate about making complex microbiological concepts accessible without sacrificing accuracy; a skill that sits at the intersection of her scientific training and her professional work in content and SEO.",78,{"slug":116,"name":117,"description":118,"image":119,"body":120,"postCount":121},"sushmita-baniya","Sushmita Baniya","Author \u002F Contributor","https:\u002F\u002Fassets.microbeonline.com\u002Fauthors\u002Fsushmita-baniya-1.png","Sushmita Baniya holds an M.Sc. in Medical Microbiology from Tribhuvan University (National College), with a research focus in Genetics and Molecular Biology. She is actively involved in teaching and research in the field of microbiology.",26,{"slug":123,"name":124,"description":118,"image":125,"body":126,"postCount":127},"samikshya-acharya","Samikshya Acharya","https:\u002F\u002Fassets.microbeonline.com\u002Fauthors\u002Fsamikshya-acharya.jpeg","Samikshya Sharma completed her postgraduate studies in Medical Microbiology at the Central Department of Microbiology, Tribhuvan University, Nepal. She contributes to Microbeonline with the goal of making foundational and clinical microbiology concepts clear and useful for students in medical, laboratory science, and allied health programs.",20,{"slug":129,"name":130,"description":118,"image":42,"body":131,"postCount":132},"alisha-tripathi","Alisha Tripathi","Alisha Tripathi holds an M.Sc. in Medical Microbiology from National College, Tribhuvan University. With over a year of teaching experience, her academic interests span Molecular Biology, Immunology, and Genetics.",6,{"slug":134,"name":135,"description":136,"image":42,"body":137,"postCount":138},"aastha-shrestha","Aastha Shrestha"," Author \u002F Contributor","Aastha Shrestha is a Biotechnology graduate with an M.Sc. from National College, Tribhuvan University. Her academic interests center on Molecular Biology and Immunology; two fields that are increasingly converging in modern diagnostic and clinical microbiology. \n\nShe contributes to Microbeonline with the goal of making complex concepts in these areas approachable and exam-relevant for students across medical, biotechnology, and laboratory science programs.",9,{"slug":140,"name":141,"description":142,"image":42,"body":42,"postCount":143},"guest-author","Guest Author","Guest Author \u002F Contributor",1,{"slug":145,"name":146,"description":118,"image":147,"body":148,"postCount":149},"srijana-khanal","Srijana Khanal","https:\u002F\u002Fassets.microbeonline.com\u002Fauthors\u002Fsrijana-khanal-1.png","Srijana Khanal is a microbiology educator with nearly a decade of teaching experience, including her role as faculty in the Microbiology Department at National College, NIST. \n\nHer time in the classroom has given her a clear sense of where students struggle and what explanations actually work, a perspective that directly shapes how she writes.\n\nHer academic interests span Immunology, Genetics, Basic Sciences, and Research Methodology, and she brings the same rigor to her writing that she brought to teaching. Alongside academic writing, she has a passion for creative writing -- an instinct that shows in her ability to make dense scientific material readable without sacrificing accuracy.\n\nShe contributes to Microbeonline to extend her teaching reach beyond the classroom, helping medical and laboratory science students across the region build a stronger foundation in microbiology.",17,{"slug":151,"name":152,"description":142,"image":42,"body":42,"postCount":143},"dr-poonam-acharya","Dr. Poonam Acharya",{"slug":154,"name":155,"description":156,"image":157,"body":158,"postCount":159},"nisha-rijal","Nisha Rijal","Microbiologist and AMR Specialist Kathmandu, Nepal","https:\u002F\u002Fassets.microbeonline.com\u002Fauthors\u002Fnisha-rijal-1.png","Nisha Rijal is a microbiologist with nearly 15 years of frontline diagnostic and surveillance experience at the National Public Health Laboratory (NPHL), national reference laboratory under the Department of Health Services, Nepal. She currently works as an AMR Support Officer at the World Health Organization (WHO), Nepal, where her work focuses on strengthening antimicrobial resistance surveillance systems and translating AMR data into actionable public health response.\n\nHer research, published in peer-reviewed journals and cited over 220 times, spans some of the most clinically significant infectious disease challenges in Nepal and South Asia: antimicrobial resistance trends in *Vibrio cholerae* across an 11-year national surveillance dataset, sero-epidemiology of scrub typhus in patients with acute febrile illness, lower respiratory tract infections in HIV-positive patients, and gonococcal resistance surveillance. She was a contributor to Nepal's National Antimicrobial Resistance Containment Action Plan, a foundational policy document for AMR governance in Nepal. You can find list of [Nisha Rijal's article here in Google Scholar.](https:\u002F\u002Fscholar.google.com\u002Fcitations?user=N-Ruq54AAAAJ&hl=en)\n\nThis depth of experience is visible in her writing at Microbeonline. Her 53 published articles cover bacteriology, parasitology, mycology, immunology, and laboratory techniques, and are consistently among the most detailed and clinically grounded content on the site. She brings to every article the same standard that national reference laboratory work demands: methodological precision, awareness of real diagnostic constraints, and an understanding of what results actually mean for patient care in resource-limited settings.\n\nHer areas of particular expertise include antimicrobial susceptibility testing and resistance mechanism detection, quality assurance in clinical microbiology, and laboratory-based infectious disease surveillance.\n\n---\n\n*Nisha Rijal contributes to Microbeonline in a personal capacity. Her views and writing do not represent the positions of the World Health Organization or any other institution.*",54,{"slug":161,"name":162,"description":163,"image":164,"body":165,"postCount":143},"padma-shrestha","Padma Shrestha","Author","https:\u002F\u002Fassets.microbeonline.com\u002Fauthors\u002Fpadma-shrestha.png","Padma Shrestha is from Kathmandu, Nepal. She has completed Masters degree in Medical microbiology from Tribhuvan University. She has great interest in Microbiology and Molecular Biology.",[167,174,180,185,190,195,199,203,207,212,216,221,225,230,235,239,243,247,252,257,261,265,269,274,278,282,286,290,295,300,304,308,312,316,320,324,328,332,336,340,344,348,352,356,360,364,368,372,377,381,385,389,393,397,401,405,409,413,417,421,425,429,433,437,441,445,449,453,456,460],{"slug":168,"name":169,"description":170,"image":171,"body":172,"postCount":173},"gram-negative-cocci","Gram-Negative Cocci and Coccobacilli","Neisseria, Moraxella, Haemophilus and related gram-negative coccal organisms","https:\u002F\u002Fassets.microbeonline.com\u002Ftags\u002Fgram-negative-cocci.png","# Gram Negative Cocci\n\nNeisseria gonorrhoeae, Neisseria meningitides, Moraxella catarrhalis, and other Neisseria spp. are clinically relevant gram-negative cocci.\n\nN. gonorrhoeae is the leading cause of sexually transmitted disease whereas N. meningitides is a leading cause of fatal bacterial meningitis.",14,{"slug":175,"name":176,"description":177,"image":42,"body":178,"postCount":179},"microscopy","Microscopy","Microscope types, components, and microscopy techniques","These are list of blog posts related to microscopy. ",12,{"slug":181,"name":182,"description":183,"image":42,"body":42,"postCount":184},"gram-positive-cocci","Gram-Positive Cocci","Staphylococcus, Streptococcus, Enterococcus, Micrococcus — organisms, diseases, and identification tests",11,{"slug":186,"name":187,"description":188,"image":42,"body":42,"postCount":189},"gram-negative-rods","Gram-Negative Rods (Other than Enterobacteriaceae)","\u003Cp>Gram negative rods other than members of Enterobacteriaceae family such as  Pseudomonas, Acinetobacter and related organisms\u003C\u002Fp>",5,{"slug":191,"name":192,"description":193,"image":42,"body":42,"postCount":194},"gram-positive-rods","Gram-Positive Rods","Bacillus, Clostridium, Listeria, Corynebacterium, Actinomyces and related organisms",8,{"slug":196,"name":197,"description":198,"image":42,"body":42,"postCount":184},"mycobacteria","Mycobacteria","Mycobacterium tuberculosis, leprosy, atypical mycobacteria, and acid-fast organism diagnosis",{"slug":200,"name":201,"description":202,"image":42,"body":42,"postCount":184},"anaerobic-bacteriology","Anaerobic Bacteriology","Anaerobic organisms, anaerobic culture methods, and anaerobic infection diagnosis",{"slug":204,"name":205,"description":206,"image":42,"body":42,"postCount":179},"enterobacteriaceae","Enterobacteriaceae","Identification, differentiation, and clinical significance of Enterobacteriaceae family members",{"slug":208,"name":209,"description":210,"image":42,"body":42,"postCount":211},"spirochetes","Spirochetes","Treponema, Leptospira, Borrelia and spirochetal infections",7,{"slug":213,"name":214,"description":215,"image":42,"body":42,"postCount":173},"food-microbiology","Food Microbiology","Food-borne pathogens, food safety, spoilage, and preservation",{"slug":217,"name":218,"description":219,"image":42,"body":42,"postCount":220},"antimicrobial-susceptibility-testing","Antimicrobial Susceptibility Testing","Methods for testing antibiotic susceptibility in clinical microbiology",21,{"slug":222,"name":223,"description":224,"image":42,"body":42,"postCount":194},"antimicrobials-moa-amr","Antimicrobials (MOA & AMR)","Mechanisms, detection, and clinical significance of antimicrobial resistance",{"slug":226,"name":227,"description":228,"image":42,"body":42,"postCount":229},"sterilization-disinfection","Sterilization and Disinfection","Methods of sterilization and disinfection in healthcare and laboratory settings",10,{"slug":231,"name":232,"description":233,"image":42,"body":42,"postCount":234},"specimen-collection-transport","Specimen Collection and Transport","Collection, handling, and transport of clinical specimens for microbiological testing",27,{"slug":236,"name":237,"description":238,"image":42,"body":42,"postCount":220},"bacterial-structure-physiology","Bacterial Structure and Physiology","Bacterial cell structure, growth, physiology, and environmental factors affecting growth",{"slug":240,"name":241,"description":42,"image":42,"body":242,"postCount":132},"horizontal-gene-transfer","Horizontal Gene Transfer","Articles related to **Horizontal Gene Transfer**",{"slug":244,"name":245,"description":42,"image":42,"body":246,"postCount":229},"chromatography","Chromatography","Information about chromatographic techniques.",{"slug":248,"name":249,"description":250,"image":42,"body":251,"postCount":211},"electrophoresis","Electrophoresis","Information about Electrophoresis Techniques ","Detailed information  about Electrophoresis Techniques ",{"slug":253,"name":254,"description":255,"image":42,"body":256,"postCount":132},"pcr-techniques","PCR Techniques","Information about various types of Polymerase Chain Reaction Techniques ","More detailed information about various types of Polymerase Chain Reaction Techniques ",{"slug":258,"name":259,"description":260,"image":42,"body":42,"postCount":132},"bacteriophage","Bacteriophage","Description about Bacteriophage.",{"slug":262,"name":263,"description":264,"image":42,"body":42,"postCount":132},"malaria","Malaria","It is the collections of articles regarding malarial disease. ",{"slug":266,"name":267,"description":268,"image":42,"body":42,"postCount":132},"anaerobic-culture-techniques","Anaerobic Culture Techniques","Posts related with Anaerobic Culture Techniques.",{"slug":270,"name":271,"description":272,"image":42,"body":42,"postCount":273},"immunoassays","Immunoassays","You will get information about all the diagnostic tests that rely on the specific binding between an antigen and an antibody to detect or quantify a substance.",19,{"slug":275,"name":276,"description":277,"image":42,"body":42,"postCount":211},"biosafety-levels","Biosafety levels ","Articles related to Biosafety Levels",{"slug":279,"name":280,"description":281,"image":42,"body":42,"postCount":189},"environmental-factors","Environmental Factors ","In this case we are talking about growth requirements of microorganisms with deep dive in environmental factors that affect the growth. ",{"slug":283,"name":284,"description":285,"image":42,"body":42,"postCount":132},"pipette","Pipette","Posts related with Pipette. ",{"slug":287,"name":288,"description":289,"image":42,"body":42,"postCount":194},"bacteriology-mcqs","Bacteriology MCQs","This sections lists MCQs in Bacteriology.",{"slug":291,"name":292,"description":293,"image":42,"body":42,"postCount":294},"parasitology-mcqs","Parasitology MCQs","This section lists MCQs in Parasitology.",2,{"slug":296,"name":297,"description":298,"image":42,"body":42,"postCount":299},"virology-mcqs","Virology MCQs","This is the collections of Multiple Choice Questions in Virology.",4,{"slug":301,"name":302,"description":303,"image":42,"body":42,"postCount":189},"mcqs-in-microbiology","MCQs in Microbiology","This section lists the collections of Multiple Choice Questions in General Microbiology Topics. ",{"slug":305,"name":306,"description":307,"image":42,"body":42,"postCount":194},"immunology-mcqs","Immunology MCQs","In this section; we are posting collections of Multiple Choice Questions about Immunology. ",{"slug":309,"name":310,"description":311,"image":42,"body":42,"postCount":138},"microbial-curiosities","Microbial Curiosities","In this clusters, we are posting interesting and unique information about Microorganisms. ",{"slug":313,"name":314,"description":315,"image":42,"body":42,"postCount":220},"bacterial-culture-media","Bacterial Culture Media","Posts related to Bacterial Culture Media. ",{"slug":317,"name":318,"description":319,"image":42,"body":42,"postCount":132},"fungal-culture-media","Fungal Culture Media","Posts related to Fungal Culture Media.",{"slug":321,"name":322,"description":323,"image":42,"body":42,"postCount":189},"motility-test","Motility Test","This lists the procedure regarding various tests methods for bacterial motility.",{"slug":325,"name":326,"description":327,"image":42,"body":42,"postCount":229},"bacterial-enumeration","Bacterial enumeration","These posts are related to isolation and enumeration of bacteria. ",{"slug":329,"name":330,"description":331,"image":42,"body":42,"postCount":294},"gram-positive-coccobacillus","Gram-positive coccobacillus","List of Gram Positive Coccobacilli",{"slug":333,"name":334,"description":335,"image":42,"body":42,"postCount":299},"dimorphic-fungi","Dimorphic Fungi","This is about various dimorphic fungi. ",{"slug":337,"name":338,"description":339,"image":42,"body":42,"postCount":211},"bacterial-classification","Bacterial Classification","These posts are related with various approaches used for the classification of Bacteria. ",{"slug":341,"name":342,"description":343,"image":42,"body":42,"postCount":189},"immunofluorescence","Immunofluorescence ","Various Tests related to Immunofluorescence ",{"slug":345,"name":346,"description":347,"image":42,"body":42,"postCount":138},"antibody-mediated-immunity","Antibody-mediated Immunity","This clusters links the articles that are sharing insights about Antibody-mediated immunity. ",{"slug":349,"name":350,"description":351,"image":42,"body":42,"postCount":211},"hypersensitivity","Hypersensitivity","Articles related to Hypersensitivity.",{"slug":353,"name":354,"description":42,"image":42,"body":42,"postCount":355},"haemophilus","Haemophilus",3,{"slug":357,"name":358,"description":359,"image":42,"body":42,"postCount":299},"sexually-transmitted-infections-stis","Sexually transmitted infections (STIs)","This is the clusters of infections that are transmitted sexually. ",{"slug":361,"name":362,"description":363,"image":42,"body":42,"postCount":179},"adaptive-immunity","Adaptive Immunity","Blog posts related to B Cell Immunity and T Cell Immunity.",{"slug":365,"name":366,"description":367,"image":42,"body":42,"postCount":173},"fungal-diagnostics","Fungal Diagnostics","Various methods used for the Diagnosis of Fungal Infections. ",{"slug":369,"name":370,"description":371,"image":42,"body":42,"postCount":189},"laboratory-storage-and-preservation","Laboratory Storage and Preservation","Articles about Laboratory Storage of Antimicrobial Disk, Test organisms and Equipment used for this process. ",{"slug":373,"name":374,"description":375,"image":42,"body":376,"postCount":132},"laboratory-heating-equipment","Laboratory Heating Equipment","A guide to laboratory heating equipment, including hot plates, water baths, Bunsen burners, incubators, and dry baths, and how to choose the right one for each task.","Laboratory heating equipment covers the instruments that warm, melt, incubate, or sterilize samples and media in a microbiology laboratory. Each one delivers heat differently. \n\nA hot plate gives high, direct, dry heat; a water bath gives gentle, even, wet heat up to about 100°C; a Bunsen burner gives an open flame for rapid, very high heat; an incubator holds cultures at a steady temperature over hours or days; and a dry bath heats small tubes without water. Choosing the right one depends on the temperature you need, how precise it must be, and whether the sample can tolerate direct or open-flame heat.\n\nThe articles below cover each piece of heating equipment in detail, including its parts, working principle, uses, and the mistakes that most often go wrong at the bench.",{"slug":378,"name":379,"description":380,"image":42,"body":42,"postCount":194},"laboratory-glassware","Laboratory Glassware","Posts about Laboratory Glassware. ",{"slug":382,"name":383,"description":384,"image":42,"body":42,"postCount":132},"helminths","Helminths","In this section, we are covering properties, life cycle, pathogenesis and laboratory diagnosis of Helminths\u002FHelminthic infestations. ",{"slug":386,"name":387,"description":388,"image":42,"body":42,"postCount":132},"protozoan-parasite","Protozoan Parasite","In this cluster, we are covering protozoan parasites. ",{"slug":390,"name":391,"description":392,"image":42,"body":42,"postCount":143},"tests-for-gram-positive-cocci","Biochemical Tests for Gram Positive Cocci","This is the lists of Biochemical Tests that are used for Gram Positive Cocci. ",{"slug":394,"name":395,"description":396,"image":42,"body":42,"postCount":229},"bacterial-staining-technique","Bacterial Staining Technique","Lists of various staining techniques that are used to stain bacteria. ",{"slug":398,"name":399,"description":400,"image":42,"body":42,"postCount":127},"enzyme-tests","Enzyme Tests","\u003Cp>Various Biochemical Test that are based on enzymatic activity of the microorganisms. \u003C\u002Fp>",{"slug":402,"name":403,"description":404,"image":42,"body":42,"postCount":184},"carbohydrate-utilization","Carbohydrate Utilization","\u003Cp>Various biochemical tests which are related to Carbohydrate fermentation or Utilization\u003C\u002Fp>",{"slug":406,"name":407,"description":408,"image":42,"body":42,"postCount":189},"susceptibility-based-id","Susceptibility-based ID","\u003Cp>These are susceptibility based identification test such as optochin sensitivity, bacitracin sensitivity etc. \u003C\u002Fp>",{"slug":410,"name":411,"description":412,"image":42,"body":42,"postCount":299},"microbial-metabolism","Microbial Metabolism","\u003Cp>Tests about Microbial Metabolism. \u003C\u002Fp>",{"slug":414,"name":415,"description":416,"image":42,"body":42,"postCount":194},"substrate-utilization","Substrate Utilization","\u003Cp>The test in which a non-sugar carbon\u002Fnitrogen source is used or degraded (citrate, malonate, decarboxylases, indole, PAD).\u003C\u002Fp>",{"slug":418,"name":419,"description":420,"image":42,"body":42,"postCount":355},"atypical-pneumonia","Atypical Pneumonia","\u003Cp>Organisms responsible for Atypical Pneumonia. \u003C\u002Fp>",{"slug":422,"name":423,"description":424,"image":42,"body":42,"postCount":189},"antigen","Antigen","\u003Cp>Various articles related to Antigens.\u003C\u002Fp>",{"slug":426,"name":427,"description":428,"image":42,"body":42,"postCount":211},"innate-immunity","Innate Immunity","\u003Cp>Articles related to Innate Immunity. \u003C\u002Fp>",{"slug":430,"name":431,"description":432,"image":42,"body":42,"postCount":299},"respiratory-tract-infection","Respiratory Tract Infection","\u003Cp>In this cluster, you can see various etiological agents that causes respiratory tract infection. \u003C\u002Fp>",{"slug":434,"name":435,"description":436,"image":42,"body":42,"postCount":189},"torch-infection","TORCH Infection","\u003Cp>In this section; you can find articles related with TOCH infection. \u003C\u002Fp>",{"slug":438,"name":439,"description":440,"image":42,"body":42,"postCount":211},"microbiology-for-beginners","Microbiology for Beginners","\u003Cp>These articles are very basic articles, which will share general concepts in Microbiology. \u003C\u002Fp>",{"slug":442,"name":443,"description":444,"image":42,"body":42,"postCount":132},"dna-replication","DNA Replication","\u003Cp>Articles related to DNA and Replication of DNA. \u003C\u002Fp>",{"slug":446,"name":447,"description":448,"image":42,"body":42,"postCount":211},"genetic-code","Genetic Code","\u003Cp>Articles related to Genetic Code.\u003C\u002Fp>",{"slug":450,"name":451,"description":452,"image":42,"body":42,"postCount":189},"molecular-technique","Molecular Technique","\u003Cp>Posts related to Molecular Techniques. \u003C\u002Fp>",{"slug":454,"name":455,"description":42,"image":42,"body":42,"postCount":143},"colorimetric-assay","Colorimetric Assay ",{"slug":457,"name":458,"description":459,"image":42,"body":42,"postCount":189},"pharmaceutical-microbiology","Pharmaceutical Microbiology","\u003Cp>Various articles related to Pharmaceutical Microbiology\u003C\u002Fp>",{"slug":461,"name":462,"description":42,"image":42,"body":42,"postCount":355},"blood-and-immune-cells","Blood and Immune Cells"]