Microbiology: In-Depth Description

Image Credit: Scientific Frontline / AI generated

Microbiology is the scientific study of microorganisms, a diverse group of microscopic life forms that include bacteria, archaea, viruses, fungi, prions, protozoa, and algae. Collectively, these organisms function as the invisible backbone of the biosphere, influencing every ecosystem on Earth. The primary goal of this field is to understand the structure, function, genetics, and ecology of these entities, as well as their complex interactions with humans, other organisms, and the environment.

Microplastics pose a human health risk in more ways than one

Bio-beads collected near Truro.
Photo Credit Beach Guardian

A new study shows that microplastics in the natural environment are colonized by pathogenic and antimicrobial resistant bacteria. The study team calls for urgent action for waste management and strongly recommends wearing gloves when taking part in beach cleans. 

Microplastics are plastic particles less than 5mm in size and are extremely widespread pollutants. It is estimated that over 125 trillion particles have accumulated in the ocean (surface to seabed) and they have also been detected in soils, rivers, lakes, animals and the human body. 

An emerging concern associated with microplastics is the microbial communities that rapidly make their home on the particle surface, forming complex biofilms known as the “Plastisphere”. These communities may often include pathogenic (disease-causing) or antimicrobial resistant (AMR) bacteria. 

Why the "gut brain" plays a central role for allergies

This tissue section, taken from the intestine of a mouse unable to produce the neuropeptide VIP, clearly shows the striking frequency with which certain cell types occur on the intestine's surface. These include villous cells (red), mucus-producing goblet cells (yellow), Paneth cells (pink) and stem cells (green).
Image Credit: © Charité | Luisa Barleben

The intestinal nervous system, often referred to as the "gut brain", is essential in controlling digestion and maintaining the intestinal barrier. This protective layer, made up of the intestinal mucosa, immune cells and the microbiome, shields the body from the contents of the gut. Its effectiveness depends on the delicate balance among these components. If this balance is disrupted, inflammation, allergies, or chronic intestinal diseases can arise. The intestinal mucosa serves as the body’s primary defense against pathogens. While previous studies have shown that the intestinal nervous system is involved in immune responses in addition to digestion, its role in the development of intestinal epithelial cells has remained largely unclear until now. 

Stroke scientists gather more evidence for presence of ‘gut-brain axis’

Image Credit: Scientific Frontline / stock image

Research on mice by scientists at The University of Manchester has shed new light on why the guts’ immune system changes after a stroke and how it might contribute to gastro-intestinal problems. 

Published in Brain, Behavior and Immunity, the study adds to the emerging idea of the “gut-brain axis” – in which scientists suggest allows communication between the two organs in both health and disease. 

The study casts more light on the biology of stroke, a life-threatening medical emergency that disrupts blood flow to parts of the brain often causing long-term effects to mobility and cognition. 

Stroke patients are also at risk of secondary bacterial infections and often exhibit gastrointestinal symptoms including difficulty swallowing and constipation. 

Disrupting bacterial "chatter" to improve human health

Computer-rendered split image of bacteria on a tooth surface. When microbial communication is “on”, disease-associated species grow (left). Disrupting this communication (right) promotes health-associated bacteria.
Image Credit: University of Minnesota

Like all living things, bacteria adapt to survive. Over time, bacteria have been developing resistance to common antibiotics and disinfectants, which poses a growing problem for healthcare and sanitation. However, many species of bacteria are beneficial and even essential for human health. What if there was a way to change the behavior of bacteria in the body to prevent illness and poor health outcomes? 

Bacteria are very “talkative.” Constant streams of communication, known as quorum sensing, occur between and among the 700 species of bacteria that live in a human mouth. A number of them communicate via special molecules called N-acyl homoserine lactones (AHLs). 

A Microbial Blueprint for Climate-Smart Cows

Matthias Hess, with the UC Davis Department of Animal Science, and researchers at UC Berkeley, have identified which microbes in a cow's gut could help reduce methane. It brings them a step closer to engineering gut microbes to create more climate-friendly cows.
Photo Credit: Gregory Urquiaga / UC Davis

Each year, a single cow can belch about 200 pounds of methane. The powerful greenhouse gas is 27 times more potent at trapping heat in the atmosphere than carbon dioxide. For decades, scientists and farmers have tried to find ways to reduce methane without stunting the animal’s growth or productivity. 

Recent research at University of California, Davis, has shown that feeding cows red seaweed can dramatically cut the amount of methane that is produced and released into the environment. Until now, however, scientists did not fully understand how red seaweed changes the interactions among the thousands of microbes in the cow’s gut, or rumen. 

New analysis yields clearer picture of toxin-producing blue-green algae blooms

2024 cyanobacterial bloom at Detroit Reservoir
Photo Credit: Elijah Welch, city of Salem.

A long-term analysis shows that a major Oregon reservoir abruptly swapped one type of toxic algae for another midway through the 12-year study period, absent from any obvious cause. 

The project provides a novel look at harmful algal blooms, or HABs which pose multiple health risks to people and animals worldwide. 

Harmful algal blooms in lakes and reservoirs are explosions of cyanobacteria, often referred to as blue-green algae. Microscopic organisms ubiquitous in all types of water around the globe, cyanobacteria use sunlight to make their own food and in warm, nutrient-rich environments can quickly multiply, resulting in blooms that spread across the water’s surface. 

These blooms can form at any time of the year but most often occur between spring and fall. Some types of cyanobacteria produce liver toxins and neurotoxins, while others make toxins that can cause gastrointestinal illness if swallowed and acute rashes upon contact with skin. 

UQ scientists uncover secrets of yellow fever

Dr Summa Bibby
Photo Credit: The University of Queensland

University of Queensland researchers have captured the first high-resolution images of the yellow fever virus (YFV), a potentially deadly viral disease transmitted by mosquitoes that affects the liver.

They’ve revealed structural differences between the vaccine strain (YFV-17D) and the virulent, disease-causing strains of the virus.

Dr Summa Bibby from UQ’s School of Chemistry and Molecular Bioscience said despite decades of research on yellow fever, this was the first time a complete 3D structure of a fully mature yellow fever virus particle had been recorded at near-atomic resolution.

“By utilising the well-established Binjari virus platform developed here at UQ, we combined yellow fever’s structural genes with the backbone of the harmless Binjari virus and produced virus particles that could be safely examined with a cryo-electron microscope,” Dr Bibby said.

“Atlas” of mouse microbiome strengthens reproducibility of animal testing

Prof. Dr. Bahtiyar Yilmaz, Research group leader at the Department for Biomedical Research (DBMR) of the University of Bern and Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital.
Photo Credit: © Courtesy of Bahtiyar Yilmaz

Laboratory mice are indispensable for biomedical discovery, yet even genetically identical mice can yield conflicting experimental results depending on their resident microbiota. The complex interplay between microbial communities and their associated metabolic functions in the intestine can profoundly influence experimental results, therapeutic interventions, and our understanding of various biological processes. Understanding the dynamics of the gut microbiome is therefore of paramount importance for biomedical research, as it plays a vital role in shaping health and disease outcomes. This groundbreaking study addresses a fundamental question in microbiome science: how does the composition of microbial communities affect their metabolic function? By exploring this relationship, the research aims to provide insights that could lead to more effective strategies for utilizing mouse models in biomedical studies. 

Led by researchers from the Department of Biomedical Research of the University of Bern and the Department of Visceral Surgery and Medicine from the Inselspital, Bern University Hospital, this collaborative effort involved a vast global consortium, that meticulously analyzed approximately 4,000 intestinal samples from mice. The study forms the geographically most comprehensive mouse microbiome dataset to date and revealed that, despite immense differences in bacterial species across facilities, metabolic outputs in the intestine are strikingly consistent. The findings represent a significant milestone in microbiome research and were recently published in the scientific journal Cell Host & Microbe.

Researchers identify bacteria that could provide an early warning of blue-green algae toxicity

Photo Credit: Lara Jansen.

Researchers at McGill University have identified bacteria that can indicate whether a blue-green algae (cyanobacteria) bloom is likely to be toxic, offering a potential water-safety early warning system. Blooms are becoming more frequent due to climate change, according to previous McGill research. They can produce various contaminants, known as cyanotoxins, that pose serious health risks to humans, pets and wildlife.

The study was led by Lara Jansen in Professor Jesse Shapiro’s lab, in the Department of Microbiology and Immunology. It showed that bacterioplankton populations shift in proportion to the broader bacterial community during a bloom. Jansen conducted the research at McGill as a PhD student, while on exchange from Portland State University.

Some of the bacterioplankton she identified – including some related to those known to break down cyanotoxins – were consistently more abundant in toxic blooms, suggesting that shifts in these bacterial populations may indicate a need for further testing to determine whether the water in a lake has become hazardous.

What Is: The Human Microbiome

The Human Microbiome
Image Credit: Scientific Frontline stock image

The Invisible Organ

The human body is not a sterile, solitary entity. It is a dense, complex, and dynamic ecosystem. Each individual serves as a host to a vast community of microorganisms, collectively known as the human microbiota. This community, which resides in and on the body, is estimated to comprise between 10 trillion and 100 trillion symbiotic microbial cells. Early estimates, which have become a cornerstone of the field, suggested these microbial cells outnumber human cells by a ratio of ten to one. While more recent analyses propose a ratio closer to 1:1, the sheer scale of this microbial colonization remains staggering. These microbial cells, though only one-tenth to one-hundredth the size of a human cell, may account for up to five pounds of an adult's body weight.

This vast microbial community is not a passive passenger. It functions as a "virtual organ" of the body, or more precisely, a "metabolic organ". It is so deeply integrated into our physiology that we are dependent on it for essential life functions, including digestion, immune system development, and the production of critical nutrients.

Sublethal antibiotic levels found to boost spread of resistance genes in the environment by up to 45 times

Photo Credit: Daniel Quiceno M

A new study has found that exposure to sublethal levels of antibiotics, amounts too low to kill bacteria, can increase the spread of antibiotic resistance genes of Escherichia coli (E. coli) found in the environment by up to 45 times.

The study led by researchers from the University of Nottingham and Ineos Oxford Institute for antimicrobial research (IOI) analyzed 39 E. coli strains from a UK dairy farm that were resistant to a group of widely used human critical antibiotics called cephalosporins.

Their findings published in Frontiers journal, showed that all 39 cephalosporin resistant E. coli strains carried the same resistance gene- blaCTX-M-15, which protects bacteria from penicillin and cephalosporin antibiotics

Genetic testing showed the bacteria were almost identical, suggesting a single strain had spread across the farm. Researchers also found that the resistance gene wasn’t fixed in place- it could jump from the bacterial chromosome onto separate small circular double-stranded DNA molecules called plasmids, which can move between bacteria.

Rebalancing the Gut: How AI Solved a 25-Year Crohn’s Disease Mystery

Electron micrographs show how macrophages expressing girdin neutralize pathogens by fusing phagosomes (P) with the cell’s lysosomes (L) to form phagolysosomes (PL), compartments where pathogens and cellular debris are broken down (left). This process is crucial for maintaining cellular homeostasis. In the absence of girdin, this fusion fails, allowing pathogens to evade degradation and escape neutralization (right).
Image Credit: UC San Diego Health Sciences

The human gut contains two types of macrophages, or specialized white blood cells, that have very different but equally important roles in maintaining balance in the digestive system. Inflammatory macrophages fight microbial infections, while non-inflammatory macrophages repair damaged tissue. In Crohn’s disease — a form of inflammatory bowel disease (IBD) — an imbalance between these two types of macrophages can result in chronic gut inflammation, damaging the intestinal wall and causing pain and other symptoms. 

Researchers at University of California San Diego School of Medicine have developed a new approach that integrates artificial intelligence (AI) with advanced molecular biology techniques to decode what determines whether a macrophage will become inflammatory or non-inflammatory. 

The study also resolves a longstanding mystery surrounding the role of a gene called NOD2 in this decision-making process. NOD2 was discovered in 2001 and is the first gene linked to a heightened risk for Crohn’s disease.

Dangerous E. coli strain blocks gut’s defense mechanism to spread infection

Isabella Rauch, Ph.D., is the senior author on a new study published in Nature that reveals how a dangerous strain of E. coli blocks the body’s immune defenses to spread infection.
Photo Credit: OHSU/Christine Torres Hicks

When harmful bacteria that cause food poisoning, such as E. coli, invade through the digestive tract, gut cells usually fight back by pushing infected cells out of the body to stop the infection from spreading.

In a new study published today in Nature, scientists from Genentech, a member of the Roche Group, in collaboration with researchers from Oregon Health & Science University, discovered that a dangerous strain of E. coli — known for causing bloody diarrhea — can block this gut defense, allowing the bacteria to spread more easily.

The bacteria inject a special protein called NleL into gut cells, which breaks down key enzymes, known as ROCK1 and ROCK2, that are needed for infected cells to be expelled. Without this process, the infected cells can’t leave quickly, allowing the bacteria to spread more easily.

Fungal secrets of a sunken ship

Robert Blanchette, a professor at the University of Minnesota, and Claudia Chemello, president and co-founder of Terra Mare Conservation, examine the wood of the USS Cairo.
Photo Credit: Paul Mardikian

University of Minnesota researchers studied the microbial degradation of the USS Cairo, one of the first ironclad and steam powered gunboats used in the United States Civil War. Studies of microbial degradation of historic woods are essential to help protect and preserve important cultural artifacts. 

Built in 1861, the ship hit a torpedo and sank in December 1862 and was recovered about 100 years later from the Yazoo River. It's been on display at the Vicksburg National Military Park in Mississippi. Although the ship has a canopy cover, it is exposed to environmental elements. 

Dusty air is rewriting your lung microbiome

UCR researcher collecting dust from the Salton Sea.
Photo Credit: Linton Freund/UCR

Dust from California’s drying Salton Sea doesn’t just smell bad. Scientists from UC Riverside found that breathing the dust can quickly re-shape the microscopic world inside the lungs. 

Genetic or bacterial diseases have previously been shown to have an effect on lung microbes. However, this discovery marks the first time scientists have observed such changes from environmental exposure rather than a disease. 

Published in the journal mSphere, the study shows that inhalation of airborne dust collected close to the shallow, landlocked lake alters both the microbial landscape and immune responses in mice that were otherwise healthy.

“Even Salton Sea dust filtered to remove live bacteria or fungi is altering what microbes survive in the lungs,” said Mia Maltz, UCR mycologist and lead study author. “It is causing deep changes to our internal environment.”

Microbes at Red Sea vents show how life and geology shape each other

Microscopic images of the studied microbes.
Image Credit: Courtesy of King Abdullah University of Science and Technology

A new study led by King Abdullah University of Science and Technology (KAUST) Professor Alexandre Rosado has revealed an unusual microbial world in the Hatiba Mons hydrothermal vent fields of the central Red Sea, a site first discovered by one of his co-authors and colleagues, Assistant Professor Froukje M. van der Zwan. 

Published in Environmental Microbiome, the study delivers the first "genome-resolved" analysis of these hydrothermal systems, providing an unprecedented view into both the types of microbes present and the metabolic functions that sustain them. 

“Microbes from the Hatiba Mons fields show remarkable metabolic versatility,” said KAUST Ph.D. student and lead author of the study, Sharifah Altalhi. “By understanding their functions, we can see how life shapes its environment, and how geology and biology are deeply intertwined in the Red Sea.” 

“Molecular bodyguard” helps infections persist

Joram Waititu and Kemal Avican working together in the Avican Lab at the Department of Molecular Biology, Umeå University.
Photo Credit: Gabrielle Beans

Researchers at Umeå University have identified a key molecular player that helps bacteria survive the hostile environment inside the body. Their study reveals how the protein RfaH acts as a protective shield for bacterial genes — and points to new strategies for fighting persistent infections.

“The human body is a very stressful place for bacteria,” says Kemal Avican research group leader at Department of Molecular Biology and Icelab at Umeå University and leader of the study. “During infection, the immune system attacks, nutrients are scarce, and microbes are exposed to bile salts, acids and heat. We looked at how RfaH helps bacteria deal with that stress by turning on the right survival genes at the right time.”

Persistent bacterial infections pose a major challenge in medicine: bacteria can linger in the body long after acute symptoms fade, evading immune defenses and surviving antibiotic treatment. In diseases like tuberculosis, this leads to relapse and makes treatment difficult.

African Wildlife Poop Sheds Light on What Shapes the Gut Ecosystem

Photo Credit: James C. Beasley

A study of elephants, giraffes and other wildlife in Namibia’s Etosha National Park underscores the ways in which the environment, biological sex, and anatomical distinctions can drive variation in the gut microbiomes across plant-eating species. Because the gut microbiome plays a critical role in animal health, the work can be used to inform conservation efforts.

“This study is valuable because Etosha gave us the opportunity to sample such a large number of species under different environmental conditions,” says Erin McKenney, co-author of a paper on the work and an assistant professor of applied ecology at North Carolina State University. “That gives us meaningful insight into the role the environment plays in shaping the gut microbiome of herbivores.

“Unfortunately, this study may also be important for a second reason,” McKenney says. “Etosha is experiencing devastating wildfires affecting a huge section of the park. Because our samples were taken before the wildfires, these findings could inform recovery efforts by helping us understand how species’ microbiomes are adjusting to changes in diet that stem from the fire’s impact on the landscape.”

“Cocktails” of common pharmaceuticals in our waterways may promote antibiotic resistance

Photo Credit: Nana K.

New research has shown, for the first time, how mixtures of commonly used medications which end up in our waterways and natural environments might increase the development of antibiotic-resistant bacteria.

When humans or animals take medications, as much as 90 percent can pass through the body and into natural environments, via waste-water, or run-off from fields, ending up in the ocean. 

In the environment, this build-up of antibiotic medicines can accumulate to a strength sufficient to kill the bacteria that live there; this can result in bacteria evolving defenses that help them to survive these concentrations, which can mean they are also resistant to antibiotics used to treat them if they later infect humans. However, less is known about how build-up of other medicines also affects bacteria, and until now, scientists have largely investigated the effect of these medications on triggering this antibiotic resistance one-at-a-time.