Structural model at atomic resolution of bacteriophage T4
Creationism's putative creator is nothing if not obsessive.
One of its obsessions appears to be designing ever-more exquisite ways to kill its creation as almost nothing in nature exists that doesn't have something that lives on or in it, often killing it in the process or at least weakening it in some way.
Its most visible obsession seems to be with designing beetles of which there are some 500,000 species with more being discovered almost daily. It's highly likely that there may be as many as a million different beetles in the world, many of which catch and devour other arthropods.
But it's in the field of virology that we find another obsession with designing variations on a general theme. Not only are there literally hundreds of thousands of viruses but every species has multiple variants - look at the number of different variants of the SARS-CoV-2 virus that have emerged since the initial wave of the COVID-19 pandemic!
How are viruses classified and where does a variant become a new species, with examples, please? Viruses are classified based on several factors, primarily their genetic material, replication strategies, morphology, and host range. The International Committee on Taxonomy of Viruses (ICTV) is the authority responsible for viral taxonomy. Here's an outline of virus classification and when a variant becomes a new species:In a recent paper, scientists from Sydney University, Australia used AI machine learning to identify 161,979 new species of RNA virus. I'll have more to say about that piece of research in my next post, but what prompted this post was the discovery of more than 600 viruses, many of them previously unknown to science, which can be found in our bathrooms - on used toothbrushes, shower heads, etc.
Virus Classification Criteria
- Type of Genetic Material (Genome):
- DNA or RNA: Viruses can have either DNA or RNA as their genetic material.
- Single-stranded (ss) or Double-stranded (ds): DNA or RNA can be single or double-stranded.
- Sense: For RNA viruses, sense refers to whether the RNA strand is positive (can be directly translated into proteins) or negative (must be converted into a positive strand before translation).
- Morphology:
- Capsid structure: Viruses can have different shapes, such as icosahedral, helical, or complex.
- Envelope: Some viruses have a lipid envelope, while others do not (non-enveloped).
- Replication Strategy:
- Baltimore Classification: Based on how viruses replicate their genome and produce mRNA. This divides viruses into seven groups (e.g., DNA viruses, RNA viruses, retroviruses).
- Host Range:
- Viruses are classified based on the organisms they infect (e.g., plants, animals, bacteria).
- Evolutionary Lineage:
- Viruses are grouped into higher taxonomic levels like families, orders, genera, and species based on genetic similarities and evolutionary history.
From Variant to New Species
A viral variant arises when mutations occur in its genome, resulting in minor genetic changes. For a variant to be considered a new species, it must show significant differences from the original virus, typically in its genomic sequence, antigenic properties, and ecological niche.
Key criteria that may lead to defining a new species:
- Distinct Genome: Major differences in the genome (e.g., recombination or significant mutation accumulation).
- Biological Properties: Changes in virulence, host range, or mode of transmission.
- Reproductive Isolation: When two populations of a virus cannot exchange genetic material efficiently or result in non-viable hybrids.
ICTV defines a new species when a virus demonstrates these unique characteristics that are consistent and stable over time. While some variants might exhibit new traits, they are still classified under the same species unless the changes are substantial enough to warrant reclassification.
Examples:
- SARS-CoV-2 (COVID-19):
- Variants: Delta, Omicron, etc., are variants of the same species, SARS-CoV-2. While these variants differ in transmissibility and immune escape, they remain classified under the same species because they share more than 96% of their genome.
- New Species Potential: If a variant were to accumulate enough changes (e.g., new replication strategies, distinct ecological niches), it could be considered a new species, though this hasn’t happened yet with SARS-CoV-2.
- Influenza Viruses:
- Influenza A viruses are classified into subtypes based on hemagglutinin (HA) and neuraminidase (NA) proteins (e.g., H1N1, H3N2).
- New species in the influenza family arise due to major genetic shifts, like reassortment events, where viruses exchange large segments of genetic material, resulting in new lineages.
- HIV-1 vs. HIV-2:
- HIV-1 and HIV-2 are two different species of the genus Lentivirus. Though both infect humans and cause similar diseases, they are genetically distinct, with HIV-2 being less virulent and having a different evolutionary origin.
Summary
Viruses are classified based on genetic material, structure, and replication mechanisms. A viral variant becomes a new species when it diverges significantly in its genetic makeup, biological properties, and ecological behavior, as seen in examples like SARS-CoV-2 variants or influenza strains.
This was discovered by scientists working at Northwestern University, Illinois, USA who have just published their findings, open access, in the online journal, Frontiers in Microbiome. Their work is explained in a Northwestern University news release:
Viruses are teeming on your toothbrush, showerhead
There’s a jungle of ‘untapped biodiversity’ in the bathroom, a new study finds
Step aside, tropical rainforests and coral reefs, the latest hotspot to offer awe-inspiring biodiversity is in your bathroom.
In a new Northwestern-led study, microbiologists found that showerheads and toothbrushes are teeming with an extremely diverse collection of viruses — most of which have never been seen before.
Although this might sound ominous, the good news is these viruses don’t target people. They target bacteria.
The microorganisms collected in the study are bacteriophage, or “phage,” a type of virus that infects and replicates inside of bacteria. Although researchers know little about them, phage recently have garnered attention for their potential use in treating antibiotic-resistant bacterial infections. And the previously unknown viruses lurking in our bathrooms could become a treasure trove of materials for exploring those applications.
The number of viruses that we found is absolutely wild. We found many viruses that we know very little about and many others that we have never seen before. It’s amazing how much untapped biodiversity is all around us. And you don’t even have to go far to find it; it’s right under our noses.
Associate Professor Erica M. Hartmann, senior author
Division of Pulmonary and Critical Care Medicine
Department of Medicine
Feinberg School of Medicine
Northwestern University, Chicago, IL, USA.
An indoor microbiologist, Hartmann is an associate professor of civil and environmental engineering at Northwestern’s McCormick School of Engineering and a member of the Center for Synthetic Biology.
The return of ‘Operation Pottymouth’
The new study is an offshoot of previous research, in which Hartmann and her colleagues at University of Colorado at Boulder characterized bacteria living on toothbrushes and showerheads. For the previous studies, the researchers asked people to submit used toothbrushes and swabs with samples collected from their showerheads.
Inspired by concerns that a flushing toilet might generate a cloud of aerosol particles, Hartmann affectionately called the toothbrush study, “Operation Pottymouth.”
This project started as a curiosity. We wanted to know what microbes are living in our homes. If you think about indoor environments, surfaces like tables and walls are really difficult for microbes to live on. Microbes prefer environments with water. And where is there water? Inside our showerheads and on our toothbrushes.
Associate Professor Erica M. Hartmann.
What they found: An ‘incredible diversity of viruses’
After characterizing bacteria, Hartmann then used DNA sequencing to examine the viruses living on those same samples. She was immediately blown away. Altogether, the samples comprised more than 600 different viruses — and no two samples were alike.
We saw basically no overlap in virus types between showerheads and toothbrushes. We also saw very little overlap between any two samples at all. Each showerhead and each toothbrush is like its own little island. It just underscores the incredible diversity of viruses out there.
Associate Professor Erica M. Hartmann.
A potential pathogen fighter
While they found few patterns among all the samples, Hartmann and her team did notice more mycobacteriophage than other types of phage. Mycobacteriophage infect mycobacteria, a pathogenic species that causes diseases like leprosy, tuberculosis and chronic lung infections. Hartmann imagines that, someday, researchers could harness mycobacteriophage to treat these infections and others.
We could envision taking these mycobacteriophage and using them as a way to clean pathogens out of your plumbing system. We want to look at all the functions these viruses might have and figure out how we can use them.
Associate Professor Erica M. Hartmann.
Avoid overreacting: Most microbes ‘will not make us sick’
But, in the meantime, Hartmann cautions people not to fret about the invisible wildlife living within our bathrooms. Instead of grabbing for bleach, people can soak their showerheads in vinegar to remove calcium buildup or simply wash them with plain soap and water. And people should regularly replace toothbrush heads, Hartmann says. Hartmann also is not a fan of antimicrobial toothbrushes, which she said can lead to antibiotic-resistant bugs.
Microbes are everywhere, and the vast majority of them will not make us sick. The more you attack them with disinfectants, the more they are likely to develop resistance or become more difficult to treat. We should all just embrace them.
Associate Professor Erica M. Hartmann.
Abstract The average American spends 93% of their time in built environments, almost 70% of that is in their place of residence. Human health and well-being are intrinsically tied to the quality of our personal environments and the microbiomes that populate them. Conversely, the built environment microbiome is seeded, formed, and re-shaped by occupant behavior, cleaning, personal hygiene and food choices, as well as geographic location and variability in infrastructure. Here, we focus on the presence of viruses in household biofilms, specifically in showerheads and on toothbrushes. Bacteriophage, viruses that infect bacteria with high host specificity, have been shown to drive microbial community structure and function through host infection and horizontal gene transfer in environmental systems. Due to the dynamic environment, with extreme temperature changes, periods of wetting/drying and exposure to hygiene/cleaning products, in addition to low biomass and transient nature of indoor microbiomes, we hypothesize that phage host infection in these unique built environments are different from environmental biofilm interactions. We approach the hypothesis using metagenomics, querying 34 toothbrush and 92 showerhead metagenomes. Representative of biofilms in the built environment, these interfaces demonstrate distinct levels of occupant interaction. We identified 22 complete, 232 high quality, and 362 medium quality viral OTUs. Viral community richness correlated with bacterial richness but not Shannon or Simpson indices. Of quality viral OTUs with sufficient coverage (614), 532 were connected with 32 bacterial families, of which only Sphingomonadaceae, Burkholderiaceae, and Caulobacteraceae are found in both toothbrushes and showerheads. Low average nucleotide identity to reference sequences and a high proportion of open reading frames annotated as hypothetical or unknown indicate that these environments harbor many novel and uncharacterized phage. The results of this study reveal the paucity of information available on bacteriophage in indoor environments and indicate a need for more virus-focused methods for DNA extraction and specific sequencing aimed at understanding viral impact on the microbiome in the built environment.Perhaps a creationist would like to explain what appears to be overkill in the sheer number of viruses their putative designer is inflicting on the rest of its creation. Sadly, the usual excuse of 'Sin' causing genetic entropy which causes 'devolution' [sic] (© Michael J. Behe/Deception Institute) isn't open to them in this case because for something to 'devolve', as though that were remotely possible, it has to exist in the first place, and since creationism's religious dogma insists there is only one entity capable of creating things; to claim otherwise would be a serious blasphemy.
1 Introduction
Continuous interactions between humans and the built environment drive reciprocal exposure to and assembly of indoor microbiota (Young et al., 2023; Klepeis et al., 2001). Niches within the built environment continuously accrue microorganisms sourced from human occupants, outdoor environments, or a mixture of the two, and many of these communities may then serve as a source of exposure back to humans (Gilbert and Stephens, 2018). These exposures influence health and disease, including via the transmission of potential pathogens (Maamar et al., 2020). Understanding the community structure and dynamics of the built environment microbiome is key to deciphering its relationship to human health.
Previous studies have shown variations between microbiomes of different human-constructed environments and even between elements of one type of indoor environment (Yooseph et al., 2013). For example, door handles, toothbrushes, and showerheads as elements in the home environment harbor distinct yet often intersecting taxa (Ross and Neufeld, 2015; Zinn et al., 2020.1). The availability of water is a major driver of community composition, impacting not only which taxa survive in an environment but also their level of activity (Lax et al., 2019). However, even within niches experiencing prolonged periods of wetness, microbiome composition is not uniform. Whether and how human occupants interact with a niche profoundly impacts the proportion of human-associated organisms in the resulting community. For example, surfaces experiencing direct contact with human skin, e.g., touch screens or handles, tend to reflect the human skin microbiome (Hsu et al., 2016).
Studies on built environment microbiomes have largely focused on bacterial members or non-bacterial pathogens, with a few notable exceptions (Ibfelt et al., 2015.1; Prussin et al., 2019.1). Despite their importance, research on the roles viruses play in built environment is very limited. In a built environment study sampling 738 metagenomes from residences, subways, and public facilities, 66% (310/471) of recovered viral operational taxonomic units (vOTUs) were found in residences (Du et al., 2023.1). In another study carried on mass transit systems (MetaSUB), no viruses were identified consistently (in >70% of samples) in 4,728 metagenomes. Results indicated that viral populations correlated with host populations in these environments and that viral communities were distinct between surfaces and air (Du et al., 2023.1; Mason et al., 2016.1). As much as the bacterial content of the built environment lacks a common “core,” the viral content seems even more variable. In-depth studies on viromes, especially on bacteriophages, in specific built environments are needed to understand the ecological interactions between viruses and bacteria which shape the built environment microbiota.
As the number of observations and the availability of data increase, quantifying which factors shape the built environment microbiomes and the magnitude of their impact is becoming feasible. Among those factors, availability of water and the degree of human interaction are likely key. Interactions between viruses and hosts and the physical and chemical characteristics of the environment may have important impacts, especially on infrequently detected or less abundant community members. To better understand factors influencing the built environment microbiome in general and the virome in particular, we contrast showerhead and toothbrush microbiomes, as both are characterized by biofilm-based communities that likely harbor virus-host interactions and are frequently wet. However, they differ in their interaction with human occupants: while there is direct contact between toothbrushes and the human oral cavity, showerheads rarely receive any direct human inputs.
Previous studies have shown that showerheads contain both pathogens and antimicrobial resistance genes (Webster et al., 2021; Gebert et al., 2018.1). In addition, non-tuberculosis mycobacteria were shown to be overabundant in showerheads with a municipal water source. Indeed, water sources were the most important indicator of microbial community composition. In contrast, toothbrush microbiomes contain a mix of human oral-associated and environmentally sourced organisms. No strong associations were found between toothbrush microbiome composition and any available meta-data, including oral hygiene practices and storage location, but the antimicrobial resistance gene diversity was strongly related to the environmentally sourced community members (Blaustein et al., 2021.1).
The built environment microbiome is highly variable and impacted by a multitude of factors. Understanding the nature and magnitude of these impacts, including the potential role of bacteriophage in governing microbial community structure and function, is essential for informing design that promotes human and environmental health, as well as the longevity of the elements that comprise our buildings. Studying phage and their hosts using a metagenomics approach provides a better understanding of phage-bacteria interactions in biofilms and potentially facilitates biofilm control. This study assessed 96 showerhead samples and 34 toothbrush samples using metagenomic sequencing. Leveraging bioinformatic pipelines designed for virome studies, we identify phages in these environments, study their connections with bacterial communities, and characterize the potential roles they play in shaping their perspective microbiomes as well as affecting health for the humans interacting with these environments.
Huttelmaier Stefanie , Shuai Weitao , Sumner Jack , Gebert Matthew , Fierer Noah , Hartmann Erica M.
Phage communities in household-related biofilms correlate with bacterial hosts
Frontiers in Microbiomes 3 (2024) DOI: 10.3389/frmbi.2024.1396560
Copyright: © 2024 The authors.
Published by Frontiers Media S.A. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
The Malevolent Designer: Why Nature's God is Not Good
This book presents the reader with multiple examples of why, even if we accept Creationism's putative intelligent designer, any such entity can only be regarded as malevolent, designing ever-more ingenious ways to make life difficult for living things, including humans, for no other reason than the sheer pleasure of doing so. This putative creator has also given other creatures much better things like immune systems, eyesight and ability to regenerate limbs that it could have given to all its creation, including humans, but chose not to. This book will leave creationists with the dilemma of explaining why evolution by natural selection is the only plausible explanation for so many nasty little parasites that doesn't leave their creator looking like an ingenious, sadistic, misanthropic, malevolence finding ever more ways to increase pain and suffering in the world, and not the omnibenevolent, maximally good god that Creationists of all Abrahamic religions believe created everything. As with a previous book by this author, "The Unintelligent Designer: Refuting the Intelligent Design Hoax", this book comprehensively refutes any notion of intelligent design by anything resembling a loving, intelligent and maximally good god. Such evil could not exist in a universe created by such a god. Evil exists, therefore a maximally good, all-knowing, all-loving god does not.
Illustrated by Catherine Webber-Hounslow.
Available in Hardcover, Paperback or ebook for Kindle
Illustrated by Catherine Webber-Hounslow.
The Unintelligent Designer: Refuting The Intelligent Design Hoax
ID is not a problem for science; rather science is a problem for ID. This book shows why. It exposes the fallacy of Intelligent Design by showing that, when examined in detail, biological systems are anything but intelligently designed. They show no signs of a plan and are quite ludicrously complex for whatever can be described as a purpose. The Intelligent Design movement relies on almost total ignorance of biological science and seemingly limitless credulity in its target marks. Its only real appeal appears to be to those who find science too difficult or too much trouble to learn yet want their opinions to be regarded as at least as important as those of scientists and experts in their fields.
Available in Hardcover, Paperback or ebook for Kindle
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