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“Revealing Bacteria’s Hidden Past: How Machine Learning Uncovered a Timeline of Evolutionary Milestones”

Scientists have helped to construct a detailed timeline for bacterial evolution, suggesting some bacteria used oxygen long before evolving the ability to produce it through photosynthesis.

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The University of Queensland scientists have made a groundbreaking discovery that sheds light on the evolutionary history of bacteria. By combining genomic data, fossil records, and Earth’s geochemical history, researchers from the Okinawa Institute of Science and Technology, the University of Bristol, Queensland University of Technology, and UQ have constructed a detailed timeline for bacterial evolution.

The team focused on how microorganisms responded to the Great Oxygenation Event (GOE), which changed Earth’s atmosphere from mostly devoid of oxygen to one that allows humans to breathe. The GOE occurred about 2.33 billion years ago.

Establishing accurate timescales for how bacteria evolved before, during, and after the GOE had been challenging due to incomplete fossil evidence. Professor Phil Hugenholtz from UQ’s School of Chemistry and Molecular Biosciences explained that most microbial life leaves no direct fossil record.

However, the researchers found a way to address the gaps by concurrently analyzing geological and genomic records. They used machine learning to predict whether each ancestral genome used oxygen to live. This innovative approach allowed them to estimate which genes were present in ancestral genomes and when events happened.

The results show that at least three aerobic lineages appeared before the GOE, suggesting that a capacity for using oxygen evolved well before its widespread accumulation in the atmosphere. Evidence suggests that the earliest aerobic transition occurred around 3.2 billion years ago in the cyanobacterial ancestor.

Lead author Dr Adrián Arellano Davín said that by combining genomic data, fossils, and Earth’s geochemical history with cutting-edge technologies, they were able to clarify evolutionary timelines. This approach can help predict other traits that could impact the world now, such as resistance to antibiotics.

The discovery of this timeline has significant implications for our understanding of bacterial evolution and the impact of microorganisms on Earth’s ecosystems. It also highlights the importance of continued research in microbiology and the use of machine learning techniques to better understand complex biological systems.

Bacteria

Unraveling the Mystery of Post-Treatment Lyme Disease Syndrome: A Breakthrough in Understanding its Causes

Scientists believe they know what causes the treated infection to mimic chronic illness: the body may be responding to remnants of the bacteria that causes Lyme that tend to pool in the liver and joint fluid.

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For years, doctors have been puzzled by the mysterious case of post-treatment Lyme disease syndrome (PTLD), where patients who have received treatment for Lyme disease still experience severe fatigue, cognitive challenges, body pain, and arthritis. A recent study found that 14% of patients who were diagnosed and treated early with antibiotic therapy would still develop PTLD.

Now, Northwestern University scientists believe they have cracked the code to understanding the causes behind this condition. According to Brandon L. Jutras, a bacteriologist leading the research, the body may be responding to remnants of the Borrelia burgdorferi cell wall, which breaks down during treatment yet lingers in the liver.

The key lies in peptidoglycan, a structural feature of virtually all bacterial cells and a common target of antibiotics. Jutras’ team found that while peptidoglycan from other bacteria is rapidly shed after treatment, Lyme disease’s peptidoglycan persists for weeks to months. In humans, pieces of this peptidoglycan were omnipresent in the fluid of patients with Lyme arthritis, even after treatment.

The research suggests that the maladaptive response to these lingering molecules may be behind PTLD. Jutras explained that some patients have a more robust immune response, which could result in a worse disease outcome, while others’ immune systems largely ignore the molecule. This individualized response is likely influenced by genetic factors.

The findings open up new avenues for research and treatment options. Jutras hopes to develop more accurate tests for PTLD patients and refine treatment options when antibiotics have failed. He also proposes neutralizing the inflammatory molecule using monoclonal antibodies to target peptidoglycan for destruction.

With this breakthrough, scientists are one step closer to understanding and effectively treating PTLD, providing relief to millions of people worldwide affected by this debilitating condition.

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Bacteria

A New Hope for Lyme Treatment: Piperacillin Shows Promise in Eradicating Lyme Bacteria with Minimal Side Effects

Piperacillin, an antibiotic in the same class as penicillin, effectively cured mice of Lyme disease at 100-times less than the effective dose of doxycycline, the current gold standard treatment. At such a low dose, piperacillin also had the added benefit of ‘having virtually no impact on resident gut microbes.’

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The Lyme epidemic affects nearly half a million individuals in the United States each year, causing devastating acute cases and chronic symptoms like heart problems, neurological issues, and arthritis. However, early treatment with antibiotics can prevent these complications.

Researchers at Northwestern University have discovered that piperacillin, an antibiotic from the same class as penicillin, is effective in curing mice of Lyme disease at a much lower dose than the current gold standard treatment, doxycycline. At this low dose, piperacillin has virtually no impact on resident gut microbes, unlike other antibiotics that can cause troublesome side effects.

Doxycycline and generic antibiotics wreak havoc on the microbiome, killing beneficial bacteria in the gut, whereas piperacillin is more targeted and exclusive to interfering with the unique cell wall synthesis pattern common to Lyme bacteria. This makes it a promising candidate for preemptive interventions, such as single-dose shots for someone potentially exposed to Lyme after a known deer tick bite.

Brandon L. Jutras, the study’s lead researcher, notes that powerful broad-spectrum antibiotics like doxycycline are often seen as effective because they kill extracellular bacteria without considering how it might impact other beneficial microbes in the gut. However, this approach is becoming less relevant with the increasing understanding of customized medicine and personalized approaches to treating Lyme disease.

Piperacillin has already been FDA-approved for safe treatment of pneumonia, making it a potential candidate for targeted interventions against Lyme disease. The researchers screened nearly 500 medicines using a molecular framework and found that piperacillin exclusively interfered with the cell wall synthesis pattern common to Lyme bacteria, preventing growth and division, ultimately leading to its death.

Historically, piperacillin has been administered as part of a two-drug cocktail for severe strep infections. However, in this context, adding another beta-lactamase inhibitor doesn’t improve therapy but rather negatively impacts the microbiome by becoming more broadly functional against beneficial residents.

The study was supported by several organizations, including the Bay Area Lyme Foundation and the National Institutes of Allergy and Infectious Disease. Jutras hopes that this research will help in developing proactive strategies for diagnosing and treating Lyme disease, as prevention remains a significant challenge with no approved human vaccine existing.

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“Bridge to a Brighter Future: Discovering the Electric ‘Cable Bacteria’ Ca. Electrothrix yaqonensis”

Scientists have identified a novel species of bacteria that acts as electrical wiring, potentially ushering in a new era of bioelectronic devices for use in medicine, industry, food safety, and environmental monitoring and cleanup.

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Ca. Electrothrix yaqonensis, a novel species of bacteria, has been discovered in a mud flat at the Oregon coast. This breakthrough could lead to the development of bioelectronic devices for various applications, including medicine, industry, food safety, and environmental monitoring and cleanup.

Researchers from Oregon State University, led by postdoctoral researcher Cheng Li and distinguished professor emerita Clare Reimers, identified the new species in intertidal sediment samples from the Yaquina Bay estuary. The team’s findings were published in Applied and Environmental Microbiology.

Cable bacteria are known for their unique ability to conduct electricity, an adaptation that optimizes their metabolic processes in sediment environments. Ca. Electrothrix yaqonensis features a mix of metabolic pathways and genes from the Ca. Electrothrix genus and other known cable bacteria genera. This new species is distinct from others in terms of its metabolic potential and structural features.

Cheng Li noted that this new species could provide insights into how these bacteria evolved and functioned in different environments. The highly conductive fibers made of unique, nickel-based molecules enable the bacteria to perform long-distance electron transport, connecting electron acceptors with donors in deeper sediment layers.

These bacteria play a crucial role in sediment geochemistry and nutrient cycling. Their ability to transfer electrons could be used to clean up pollutants from sediments. Additionally, their design of highly conductive nickel protein might inspire new bioelectronics.

The researchers drew the name Ca. Electrothrix yaqonensis from the Yaqona people, whose ancestral lands encompassed Yaquina Bay. This acknowledges the historical bond between the tribe and the land, as well as the enduring contributions to ecological knowledge and sustainability.

The discovery of Ca. Electrothrix yaqonensis could have significant implications for various industries and environmental applications. Further research is needed to fully explore its potential and understand how these bacteria evolved to develop their unique features.

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