Tag: microbial identification

Sequence conservation and gene essentiality endow phylogenetic signals in ribosomal proteins

February 13, 2024

Microbes are invisible to the naked eye, and look similar under the microscope where diverse types of microbes could be classified into a few shape categories. Hence, there is a need for other identification and classification methods to catalogue the rich diversity of microbes on Earth. One approach is molecular phylogeny. In molecular phylogeny, the … More Sequence conservation and gene essentiality endow phylogenetic signals in ribosomal proteins

High specificity primers and probe may help microbial identification in qPCR workflows

January 18, 2023

Real-time quantitative polymerase chain reaction (qPCR) is the gold standard approach in clinical diagnostics for the detection of various microbial and viral pathogens in different clinical samples. The objective for most workflows is in detection, but depending on the specificity of the primers and probe used, qPCR could also afford single gene identification of the … More High specificity primers and probe may help microbial identification in qPCR workflows

Significant difficulties exist in obtaining complete understanding of microbial species represented in a metagenome

September 23, 2022

Metagenomics is one of the important culture-independent techniques for gaining an unbiased understanding of the ensemble of microbes present in a particular environment. The approach uses modern high throughput sequencing technology to obtain an understanding of the microbes present through DNA sequencing. However, to achieve the stated goal, the sequenced reads must be aligned to … More Significant difficulties exist in obtaining complete understanding of microbial species represented in a metagenome

Explaining the manuscript: Teaching microbial identification using MALDI-TOF MS

June 11, 2022

During master’s studies, I chanced upon a relatively new microbial identification technique that uses mass spectrometry to profile the proteins of a microbe for identification purposes. The technique is known as matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). I read a few application notes from Bruker Daltonics and picked up the technique. … More Explaining the manuscript: Teaching microbial identification using MALDI-TOF MS

Citizen science mini-project: Know your microbe through its 16S rRNA gene sequence

May 31, 2021

Microbial identification is perhaps the oldest branch of microbiology. Ever since the inception of the field of microbiology where scientists first looked at microbes through the lens of hand-made microscope, we have always wanted to compare the differences between different microbes, and give each a unique name. This thinking process is the same as that … More Citizen science mini-project: Know your microbe through its 16S rRNA gene sequence

MALDI-TOF mass spectrometry based microbial identification requires microbes to be cultivable on solid or liquid medium

September 9, 2020

Microbial identification is the core tenet of microbiology. Although qualitative in the past, the process of identifying microbes has moved into the molecular era with the advent of molecular profiling tools such as 16S rRNA sequencing and MALDI-TOF mass spectrometry identification approaches. In particular, the latter approach provides a faster route to microbial identification compared … More MALDI-TOF mass spectrometry based microbial identification requires microbes to be cultivable on solid or liquid medium

MALDI-TOF mass spectrometry based microbial identification is sensitive to cultivation conditions of microbes that may yield extraneous protein peaks

September 7, 2020

MALDI-TOF mass spectrometry microbial identification has moved from the research lab to the clinical microbiology laboratory. Armed with a comprehensive reference mass spectra library, the technique affords fast and easy identification of many microbes of interest to clinical microbiology. However, the approach is very sensitive to the culture conditions of microbes, and may require expert … More MALDI-TOF mass spectrometry based microbial identification is sensitive to cultivation conditions of microbes that may yield extraneous protein peaks

Difficulty in culturing marine microorganisms

June 17, 2020

The Earth’s surface is covered with water to a large extent, which implies that there is a large resource of marine microbes that could be tapped for various biotechnological applications such as production of drugs or useful compounds. However, we know relatively little of the marine microbes at the cell culture level. Although metagenomics tools … More Difficulty in culturing marine microorganisms

Cluster analysis of microbial mass spectra could not infer phylogenetic relationships

August 23, 2018

Cluster analysis classify entities based on their degree of similarity. In the area of mass spectra analysis for microbial identification, cluster analysis has been used in classifying different mass spectra depending on the extent of similarity in mass peaks profiled. However, the approach could not infer phylogenetic relationship between species. Given that mass spectra that … More Cluster analysis of microbial mass spectra could not infer phylogenetic relationships