Apa Itu Metagenomik? Bedanya Amplicon dan Shotgun, serta Contohnya di Dunia Pertanian Organik

Pendahuluan: Apa itu Metagenomik?

Metagenomik secara umum adalah studi tentang seluruh materi genetik yang ditemukan dalam suatu komunitas mikroba di lingkungan tertentu, tanpa harus melakukan isolasi dan kultur mikroorganisme satu-per-satu.

Dengan kata lain, daripada menumbuhkan bakteri di cawan dan kemudian meng­urutkan genomnya, kita melakukan ekstraksi DNA atau RNA dari seluruh komunitas mikroba (misalnya tanah, air, daun tumbuhan, usus) dan kemudian melakukan sequencing untuk mengetahui “siapa hadir” dan/atau “apa yang bisa dilakukan (fungsi)” oleh komunitas tersebut.

Metagenomik memungkinkan kita menggali ekosistem mikroba yang sebelumnya sulit atau tidak bisa dikultur — dan membuka peluang besar dalam berbagai bidang seperti ekologi mikroba, agrikultur, bioteknologi, kedokteran, lingkungan.

Namun, dalam praktiknya ada beberapa pendekatan berbeda — dua yang paling umum adalah amplicon metagenomics dan shotgun metagenomics. Kedua pendekatan ini memiliki kelebihan dan kelemahan, serta cocok untuk jenis pertanyaan riset yang berbeda.

 

🔬 Exploring NCBI BLAST: The Engine Behind Modern Bioinformatics

Have you ever wondered how scientists compare DNA or protein sequences across thousands of organisms in seconds? Welcome to NCBI BLAST — one of the most powerful and widely used bioinformatics tools in the world.

🧠 What Is NCBI BLAST?

BLAST stands for Basic Local Alignment Search Tool. It’s an algorithm developed by the National Center for Biotechnology Information (NCBI) to compare biological sequences such as DNA, RNA, or proteins against a massive database of known sequences.

Overview of Popular Bioinformatics Databases: Unveiling the Treasures of Genomic Knowledge

 

Introduction

Bioinformatics databases have become indispensable tools in genomics research, enabling scientists to manage, analyze, and explore the vast amount of genomic data generated by high-throughput sequencing technologies. These databases serve as virtual storehouses of genomic information, offering researchers access to curated data, analysis tools, and annotation resources. In this article, I will provide an overview of some of the most popular bioinformatics databases, highlighting their key features, applications, and contributions to genomic research. By unveiling the treasures of genomic knowledge hidden within these databases, I aim to empower researchers and enthusiasts in pursuing scientific discoveries. 

Bioinformatics: A Comprehensive Introduction to the Power of Data in Biology

In the era of big data and scientific advancements, biology has become increasingly reliant on computational tools and techniques to make sense of the vast amount of information generated. This interdisciplinary field, known as bioinformatics, combines biology, computer science, statistics, and data analysis to gather, organize, and interpret biological data. 

Bioinformatics has revolutionized the way we study and understand living organisms, from unraveling the complexities of the human genome to predicting the structure and function of proteins. In this article, we will provide a comprehensive introduction to bioinformatics and explore its importance in modern biological research.

Translational Bioinformatics to Accelerate the Life Sciences Research

Bioinformatics is an interdisciplinary science which develops algorithms and software tools for analyzing and understanding large amounts of biological information. It is a highly interdisciplinary field combining diverse types of specialists, including biologist, molecular life scientists, computer scientists, statisticians, and mathematicians.

 

Figure source: https://www.applicationnexus.com/bioinformatics/

Analisis Filogenetik dan Identifikasi Bakteri dengan Metode Molekuler

       

         Metode identifikasi bakteri secara garis besar dapat dibagi menjadi teknik (1) genotipik yang berdasarkan pada profil materi genetik suatu organisme (utamanya DNA) dan (2) teknik fenotipik yang berdasarkan pada profil sifat metabolik maupun beberapa aspek komposisi kimianya.  Sebelum berkembangnya teknik biologi molekuler, mikrobia dikarakterisasi berdasarkan sifat morfologi, fisiologi, dan koloninya. Biotyping, serotyping, bacteriocin typing, phage typing, pola kerentanan terhadap anti mikrobia, dan metode berbasis protein lainnya merupakan contoh metode fenotipik yang umumnya digunakan (Fakruddin, 2013).