Name: reading microbial family trees
Uploaded: 2026-03-12T13:57:34.000Z
Duration: 1 min 28 s
Channel: JoVE

Un albero filogenetico rappresenta le relazioni evolutive tra microrganismi e spesso si basa su sequenze di DNA, RNA o proteine.Nei filogrammi, le specie compaiono alle punte e la lunghezza dei rami riflette la quantità di cambiamento della sequenza.Gli alberi radicati segnano antenati comuni e punti di divergenza, mentre gli alberi non radicati mostrano legami senza direzione evolutiva.Gli alberi filogenetici utilizzano sequenze omologhe, in particolare gli ortologi, che sono geni omologhi separati dalla speciazione.I geni rRNA di piccole subunità altamente conservati, come il gene 16S rRNA, fungono da marcatori universali per i confronti microbici.Il DNA di questi geni marcatori nei campioni viene sequenziato.Le sequenze sono allineate per identificare disallineamenti e lacune derivanti da inserimenti o cancellazioni.Successivamente, la distanza evolutiva viene misurata come il rapporto tra le differenze dei nucleotidi e il numero totale di posizioni allineate.Gli alberi filogenetici possono talvolta essere fuorvianti quando caratteristiche simili si evolvono indipendentemente o quando il trasferimento genico orizzontale introduce geni attraverso linee non correlate, producendo storie geniche che non riflettono la storia evolutiva reale degli organismi.

filogenesi microbica

Comprendere le relazioni evolutive tra microrganismi è fondamentale per l'ecologia microbica e la tassonomia. Gli alberi filogenetici sono strumenti essenziali per dedurre queste relazioni, basandosi principalmente su analisi comparative di sequenze molecolari come DNA, RNA o proteine. Negli studi microbici, questi alberi tipicamente rappresentano i percorsi evolutivi di diverse specie batteriche e archeali mappando le differenze genetiche accumulate nel tempo.Gli alberi filogenetici sono composti da punte, rami e nodi. Le punte rappresentano specie esistenti o campionate, mentre i rami tracciano traiettorie evolutive. Le lunghezze dei rami sono proporzionali al numero di cambiamenti genetici inferiti tra i nodi. Gli alberi radicati evidenziano un antenato comune e una divergenza direzionale, mentre gli alberi non radicati mostrano semplicemente la parentela senza assumere un punto di origine. I nodi interni rappresentano forme ancestrali ipotetiche e possono segnare eventi di speciazione o divergenza.Nella filogenetica microbica, i geni altamente conservati—in particolare il piccolo RNA ribosomale subunitario (rRNA SSU)—sono comunemente utilizzati a causa della loro presenza in tutti i domini della vita e del lento tasso evolutivo. Questi marcatori genetici universali permettono confronti su ampie distanze filogenetiche. Vengono selezionati geni omologhi, e preferibilmente ortologi, per la costruzione degli alberi, per garantire che le sequenze condividano un'ascendenza e una funzione comuni. Gli ortologhi vengono tipicamente identificati tramite ricerche reciproche di best-hit (ad esempio, BLAST) o pipeline ortologiche, poi amplificati tramite primer specifici per il locus (o arricchimento mirato) tra i taxa. Gli ampliconi o frammenti arricchiti risultanti vengono poi sequenziati (spesso utilizzando piattaforme ad alta produttività) e filtrati per la qualità. Queste sequenze sono allineate per rilevare sostituzioni, inserzioni o delezioni in posizioni omologhe. Le distanze evolutive sono quantificate dal grado di divergenza della sequenza.Sebbene gli alberi filogenetici offrano intuizioni fondamentali, potrebbero non riflettere sempre le vere storie evolutive. I trasferimenti genici orizzontali possono portare a somiglianze fuorvianti. Per affrontare questo problema, metodi come la parsimonia massima valutano gli allineamenti delle sequenze per dedurre alberi che richiedono il minor numero di cambiamenti evolutivi. Altri approcci, come la massima verosimiglianza e l'inferenza bayesiana, sono anch'essi comunemente utilizzati per la costruzione degli alberi e spesso forniscono modelli di evoluzione statisticamente più robusti.

Filogenesi microbica

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools ...

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Education

Didattica

JoVE Core

Microbiology

Microbiologia

Unit

Unità

Microbial Evolution

Evoluzione microbica

KEY TERMS AND CONCEPTS

TERMINI E CONCETTI CHIAVE

Microbial Phylogeny

reading microbial family trees

Reading microbial family trees helps scientists study how microorganisms are related. These trees are important in microbial ecology and taxonomy. They use molecular sequences such as DNA, RNA, or proteins to compare bacteria and archaea and trace genetic changes over time.

A phylogenetic tree has tips, branches, and nodes. The tips are the species that are sampled or still alive. The branches show evolutionary paths, and branch length reflects the number of genetic changes between nodes. Rooted trees show a common ancestor and a direction of divergence, while unrooted trees show relatedness without naming an origin point. Internal nodes stand for hypothetical ancestors and can represent speciation or other divergence events.

Microbial phylogenetics often relies on highly conserved genes. Small subunit ribosomal RNA, or SSU rRNA, is a common marker because it is found across all domains of life and changes slowly. These universal markers make it possible to compare organisms that are very far apart on the evolutionary tree. Researchers choose homologous genes, and preferably orthologous genes, so the sequences share common ancestry and function.

To build a tree, scientists first identify orthologs with reciprocal best-hit searches such as BLAST or with orthology pipelines. They then use locus-specific primers or targeted enrichment to amplify the genes across taxa. The resulting amplicons or enriched fragments are sequenced, often with high-throughput platforms, and quality-filtered before analysis.

Next, the sequences are aligned so scientists can spot substitutions, insertions, and deletions at matching positions. Evolutionary distance is estimated from how much the sequences differ. Even so, a tree may not always show the true history of a group, because horizontal gene transfer can create misleading similarities. To reduce that problem, scientists may use maximum parsimony, which chooses the tree with the fewest changes. Maximum likelihood and Bayesian inference are also common methods, and they often give more statistically robust models of evolution.

Reading Microbial Family Trees

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origin of photosynthesis

How Photosynthesis Changed Earth

Photosynthesis changed Earth’s atmosphere and made complex life possible. It began about 3.4 to 3.8 billion years ago, when the first photosynthetic organisms used light energy to build organic compounds. These early organisms were anoxygenic phototrophs, which means they made food from light but did not release oxygen. Early photosynthesis used hydrogen sulfide (H2S) or ferrous iron (Fe2+) as electron donors instead of water. Because of that, it did not produce molecular oxygen (O2) as a...

evolutionary processes in microbes

How Microbes Gain New Traits

Microbes gain new traits through fast genetic change. Their short generation times help evolution happen quickly. Mutation, horizontal gene transfer, recombination, and genetic drift all contribute to this process. Together, these mechanisms help microbial populations adjust to changing environments. Horizontal gene transfer, or HGT, moves genes between different species. It happens in three main ways: conjugation, transformation, and transduction. Conjugation requires direct cell-to-cell...

evolution of new traits in microbes

Microbial Adaptation in Changing Environments

Microbial adaptation in changing environments can happen very quickly. Microorganisms often evolve fast because they have large population sizes and short generation times. In the lab, these changes can sometimes be measured within days. Natural selection acts on standing genetic variation, which is the genetic diversity already present in a population. When conditions change, helpful traits can be kept and increased because they improve fitness. This lets microbes respond to new pressures...

evolution of microbial genome

Microbial Core and Pan-Genome Changes

Microbial genomes change through gene gain and gene loss. These changes help microbes adapt to new environments and to other organisms they live with. In many species, genome evolution is fast and ongoing. A key idea is the difference between the core genome and the pan-genome. The core genome is the set of genes shared by all sampled strains of a species. These genes support basic cell functions. For example, Salmonella enterica has about 2,800 core genes, although the exact number can change...

microbial phylogeny

Reading microbial family trees helps scientists study how microorganisms are related. These trees are important in microbial ecology and taxonomy. They use molecular sequences such as DNA, RNA, or proteins to compare bacteria and archaea and trace genetic changes over time. A phylogenetic tree has tips, branches, and nodes. The tips are the species that are sampled or still alive. The branches show evolutionary paths, and branch length reflects the number of genetic changes between nodes.

phylogenetic species concept in microbiology

phylogenetic-species-concept-in-microbiology

How DNA Defines Microbial Species

The phylogenetic species concept helps define microbial species by looking at DNA and evolutionary relatedness. It focuses on shared ancestry and genetic traits that can be diagnosed in different organisms. This approach is especially useful in microbiology, where other species concepts often do not work well. Traditional morphological and biological species concepts rely on body form or reproduction. Those methods can fall short for microbes because many reproduce asexually, show little...

key terms and concepts

Learn how microbial phylogenetic trees use DNA, RNA, and protein sequences to show relationships among bacteria and archaea, and how scientists build them.

Reading Microbial Family Trees | JoVE K12

JoVE Core Microbiology provides an engaging introduction to the microbial world and its influence on health, industry, and the environment. This comprehensive collection covers key concepts such as microbial structure, metabolism, genetics, and ecology. It introduces essential laboratory techniques and microscopy methods through visually engaging animations. Corresponding scientist-in-action videos bridge classroom concepts with real-world research and applications.

microbiology

Reading Microbial Family Trees

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