Tag Archives: Digestion

Swiss researchers identify plastic-degrading microbial strains in the Alps and Arctic region

Finding, cultivating, and bioengineering organisms that can digest plastic not only aids in the removal of pollution, but is now also big business. Several microorganisms that can do this have already been found, but when their enzymes that make this possible are applied at an industrial scale, they typically only work at temperatures above 30 °C. The heating required means that industrial applications remain costly to date, and aren’t carbon-neutral. But there is a possible solution to this problem: finding specialist cold-adapted microbes whose enzymes work at lower temperatures.

Scientists from the Swiss Federal Institute WSL knew where to look for such micro-organisms: at high altitudes in the Alps of their country, or in the polar regions. Their findings are published in Frontiers in Microbiology.

“Here we show that novel microbial taxa obtained from the ‘plastisphere’ of alpine and arctic soils were able to break down biodegradable plastics at 15 °C,” said first author Dr Joel Rüthi, currently a guest scientist at WSL. “These organisms could help to reduce the costs and environmental burden of an enzymatic recycling process for plastic.”

Rüthi and colleagues sampled 19 strains of bacteria and 15 of fungi growing on free-lying or intentionally buried plastic (kept in the ground for one year) in Greenland, Svalbard, and Switzerland. Most of the plastic litter from Svalbard had been collected during the Swiss Arctic Project 2018, where students did fieldwork to witness the effects of climate change at first hand. The soil from Switzerland had been collected on the summit of the Muot da Barba Peider (2,979 m) and in the valley Val Lavirun, both in the canton Graubünden.

The scientists let the isolated microbes grow as single-strain cultures in the laboratory in darkness and at 15 °C and used molecular techniques to identify them. The results showed that the bacterial strains belonged to 13 genera in the phyla Actinobacteria and Proteobacteria, and the fungi to 10 genera in the phyla Ascomycota and Mucoromycota.

Surprising results

They then used a suite of assays to screen each strain for its ability to digest sterile samples of non-biodegradable polyethylene (PE) and the biodegradable polyester-polyurethane (PUR) as well as two commercially available biodegradable mixtures of polybutylene adipate terephthalate (PBAT) and polylactic acid (PLA).

None of the strains were able to digest PE, even after 126 days of incubation on these plastics. But 19 (56%) of strains, including 11 fungi and eight bacteria, were able to digest PUR at 15 °C, while 14 fungi and three bacteria were able to digest the plastic mixtures of PBAT and PLA. Nuclear Magnetic Resonance (NMR) and a fluorescence-based assay confirmed that these strains were able to chop up the PBAT and PLA polymers into smaller molecules.

“It was very surprising to us that we found that a large fraction of the tested strains was able to degrade at least one of the tested plastics,” said Rüthi.

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The best performers were two uncharacterized fungal species in the genera Neodevriesia and Lachnellula: these were able to digest all of the tested plastics except PE. The results also showed that the ability to digest plastic depended on the culture medium for most strains, with each strain reacting differently to each of four media tested.

Side-effect of ability to digest plant polymers

How did the ability to digest plastic evolve? Since plastics have only been around since the 1950s, the ability to degrade plastic almost certainly wasn’t a trait originally targeted by natural selection.

Microbes have been shown to produce a wide variety of polymer-degrading enzymes involved in the break-down of plant cell walls. In particular, plant-pathogenic fungi are often reported to biodegrade polyesters, because of their ability to produce cutinases which target plastic polymers due their resemblance to the plant polymer cutin.”

Dr Beat Frey, Last Author, Senior Scientist and Group Leader, WSL

Challenges remain

Since Rüthi et al. only tested for digestion at 15 °C, they don’t yet know the optimum temperature at which the enzymes of the successful strains work.

“But we know that most of the tested strains can grow well between 4 °C and 20 °C with an optimum at around 15 °C,” said Frey.

“The next big challenge will be to identify the plastic-degrading enzymes produced by the microbial strains and to optimize the process to obtain large amounts of proteins. In addition, further modification of the enzymes might be needed to optimize properties such as protein stability”.

Journal reference:

de Freitas, A. S. et al. (2023). Amazonian dark earths enhance the establishment of tree species in forest ecological restoration. Frontiers in Soil Science. doi.org/10.3389/fsoil.2023.1161627.

The Anatomy of the Human Gut: More Different Than We Thought

A recent study discovered substantial disparities in the structure of the human digestive system, with substantial variations possible even among healthy individuals. This discovery sheds light on the impact that the anatomy of the digestive tract can have on human health and provides potential avenues for medical diagnoses and a deeper understanding of the gut’s microbial ecosystem.

“There was research more than a century ago that found variability in the relative lengths of human intestines, but this area has largely been ignored since then,” says Amanda Hale, co-first author of the study and a Ph.D. candidate at North Carolina State University. “When we began exploring this issue, we were astonished at the extent of the variability we found.”

“If you’re talking to four different people, odds are good that all of them have different guts, in terms of the relative sizes of the organs that make up that system,” says Erin McKenney, corresponding author of the study and an assistant professor of applied ecology at NC State. “For example, the cecum is an organ that’s found at the nexus of the large and small intestine. One person may have a cecum that is only a few centimeters long, while another may have a cecum the size of a coin purse. And we found similar variability for many digestive organs.”

In another striking example, the researchers found that women tend to have longer small intestines than men.

“Because having a longer small intestine helps you extract nutrients from your diet, this finding supports the canalization hypothesis, which posits that women are better able to survive during periods of stress,” says Hale.

“Given that there is more variation in human gut anatomy than we thought, this could inform our understanding of what is driving a range of health-related issues and how we treat them,” says McKenney. “Basically, now that we know this variability exists, it raises a number of research questions that need to be explored.”

For this study, the researchers measured the digestive organs of 45 people who donated their remains to the Anatomical Gifts Program at the Duke University School of Medicine.

In addition to shedding light on the unexpected variability in human anatomy, this project also led to rediscovering the importance of teaching anatomical variation to medical students.

“It’s particularly important in medical training, because if students are only learning about a ‘normal’ or ‘average’ anatomy, that means they are not going to be familiar with the scope of human variation,” says Roxanne Larsen, co-author of the paper and an associate professor of veterinary and biomedical sciences at the University of Minnesota. “It’s increasingly clear that the medical field is moving toward individualized medicine to improve patient outcomes and overall health and well-being. Garnering experience in understanding anatomical variation can play a critical role in helping future doctors understand the importance of individualized medicine.”

“We’re excited about this discovery and future directions for the work,” McKenney says. “It underscores just how little we know about our own bodies.”

Reference: “Hidden diversity: comparative functional morphology of humans and other species” by Erin A. McKenney​​, Amanda R. Hale​, Janiaya Anderson, Roxanne Larsen, Colleen Grant and Robert R. Dunn, 24 April 2023, PeerJ.
DOI: 10.7717/peerj.15148

The study was funded by the National Science Foundation.

Study offers novel insights into reducing adverse effects of antibiotics on the gut microbiome

Antibiotics help to fight bacterial infections, but they can also harm the helpful microbes living in the gut, which can have long-lasting health consequences.

Now new research being presented at this year’s European Congress of Clinical Microbiology & Infectious Diseases (ECCMID) in Copenhagen, Denmark (15-18 April) has identified several protective drugs that may lessen the collateral damage caused by antibiotics without compromising their effectiveness against harmful bacteria.

The unique study by Dr Lisa Maier and Dr Camille V. Goemans from the European Molecular Biology Laboratory, Heidelberg, Germany and colleagues, which analyzed the effects of 144 different antibiotics on the abundance of the most common gut bacteria, offers novel insights into reducing the adverse effects of antibiotic treatment on the gut microbiome.

The trillions of microorganisms in the human gut profoundly impact health by aiding digestion, providing nutrients and metabolites, and working with the immune system to fend off harmful bacteria and viruses.

Antibiotics can damage these microbial communities, resulting in an imbalance that can lead to recurrent gastrointestinal problems caused by Clostridioides difficile infections as well as long-term health problems such as obesity, allergies, asthma and other immunological or inflammatory diseases.

Despite this well-known collateral damage, which antibiotics affect which types of bacterial species, and whether these negative side effects be mitigated has not been studied systematically because of technical challenges.

To find out more, researchers systematically analyzed the growth and survival of 27 different bacterial species commonly found in the gut following treatment with 144 different antibiotics. They also assessed the minimal inhibitory concentration (MIC) – the minimal concentration of an antibiotic required to stop bacteria from growing – for over 800 of these antibiotic-bacteria combinations.

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The results revealed that the majority of gut bacteria had slightly higher MICs than disease-causing bacteria, suggesting that at commonly used antibiotic concentrations, most of the tested gut bacteria would not be affected.

However, two widely used antibiotic classes – tetracyclines and macrolides – not only stopped healthy bacteria growing at much lower concentrations than those required to stop the growth of disease-causing bacteria, but they also killed more than half of the gut bacterial species they tested, potentially altering the gut microbiome composition for a long time.

As drugs interact differently across different bacterial species, the researchers investigated whether a second drug could be used to protect the gut microbes. They combined the antibiotics erythromycin (a macrolide) and doxycycline (a tetracycline) with a set of 1,197 pharmaceuticals to identify suitable drugs that would protect two abundant gut bacterial species (Bacteriodes vulgatus and Bacteriodes uniformis) from the antibiotics.

The researchers identified several promising drugs including the anticoagulant dicumarol, the gout medication benzbromarone, and two anti-inflammatory drugs, tolfenamic acid and diflunisal.

Importantly, these drugs did not compromise the effectiveness of the antibiotics against disease-causing bacteria.

Further experiments showed that these antidote drugs also protected natural bacterial communities derived from human stool samples and in living mice.

This Herculean undertaking by an international team of scientists has identified a novel approach that combines antibiotics with a protective antidote to help keep the gut microbiome healthy and reduce the harmful side effects of antibiotics without compromising their efficiency,” says Dr Ulrike Löber, of the Max-Delbrück-Center for Molecular Medicine in Berlin, Germany who is presenting the research at ECCMID. “Despite our promising findings, further research is needed to identify optimum and personalized combinations of antidote drugs and to exclude any potential long-term effects on the gut microbiome.

Differences in gut microbiome diversity attributed to dietary patterns in children with obesity

In a recent study published in Microbiology Spectrum, researchers found that differences in the dietary patterns of children with normal weight and those who were overweight or obese contributed to variations in the gut microbiome diversity, virulence factors of gut bacteria, and metabolic function.

Study: Virulence factors of the gut microbiome are associated with BMI and metabolic blood parameters in children with obesity. Image Credit: Africa Studio / Shutterstock.com

Study: Virulence factors of the gut microbiome are associated with BMI and metabolic blood parameters in children with obesity. Image Credit: Africa Studio / Shutterstock.com


A growing body of evidence indicates that gut microbiota has a significant role in various aspects of host metabolism, including digestion, harvesting of energy, and induction of low-grade inflammation. In addition, the genetic factors of the host, as well as other characteristics such as age, diet, immunity, and gender, influence the gut microbiome composition.

Research shows that bacterial diversity in the gut and the individual’s functional capacity vary between those with normal weight and obese individuals. Gut microbiome profile variations have also been linked to metabolic disorders, lipid accumulation, and inflammation.

Lipogenesis in the liver and the regulation of appetite through hormones are also associated with gut microbiome genes.

Aside from its role in adipogenesis, superoxide reduction, and the metabolism of vitamins, gut microbiota also regulates innate immunity and the systemic, low-grade inflammatory state that can contribute to fat deposition and obesity. Therefore, Dysbiosis, which is the imbalance of gut microbiota, combined with diet, likely has a significant role in the development of obesity.

About the study

In the present study, researchers conducted a cross-sectional analysis of data from 45 children between the ages of six and 12 to determine the association between gut microbiota and obesity.

Questionnaires were used to obtain information on dietary frequencies, gender, age, and body mass index (BMI). Based on the World Health Organization (WHO) z-scores, in which BMI is adjusted for gender and age, the children were classified into two categories of overweight and obese (OWOB) and normal weight (NW).

Data from food frequency questionnaires were used to classify the dietary habits of children into two nutritional patterns. To this end, Pattern 1 was characterized by complex carbohydrates and proteins, whereas Pattern 2 comprised simple carbohydrates and saturated fats.

Shotgun metagenomics was used to assess the taxonomic diversity of the gut microbiota and metabolic capacity from genomic deoxyribonucleic acid (DNA) extracted from fecal samples. Clade-specific markers were used for the taxonomic and functional assessment of the gut bacteria. Additionally, reverse Simpson and Shannon diversity indices were calculated.

The virulence factor database was used to screen for virulence factor genes, whereas multivariate linear modeling was used to determine the association between the taxa, virulence factors, and function of gut microbes and covariates of diet, serology, and anthropometric measurements.

Study findings

Significant differences between the alpha and beta diversity of the gut microbiota were observed between the children in the NW and OWOB groups, thus suggesting that specific phyla of bacteria contribute to higher levels of energy harvest.

Furthermore, species such as Ruminococcus species, Victivallis vadensis, Mitsuokella multacida, Alistipes species, Clostridium species, and Acinetobacter johnsonii were linked to healthier metabolic parameters.

In contrast, an increase in the abundance of bacteria such as Veillonellaceae, Lactococcus, Fusicatenibacter saccharivorans, Fusicatenibacter prausnitzii, Eubacterium, Roseburia, Dialister, Coprococcus catus, Bifidobacterium, and Bilophila was identified in children with pro-inflammatory conditions and obesity.

Bacteria such as Citrobacter europaeus, Citrobacter youngae, Klebsiella variicola, Enterococcus mundtii, Gemella morbillorum, and Citrobacter portucalensis were associated with higher lipid and sugar intake, as well as higher blood biochemistry values and anthropometric measurements.

Diets high in fats and simple carbohydrates have been associated with the abundance of Citrobacter and Klebsiella species in the gut. Moreover, previous studies have indicated that these bacterial species are potential markers of inflammation, obesity, and an increase in fasting glucose.

The metabolism of menaquinones and gamma-glutamyl was negatively associated with BMI. Furthermore, the microbiomes of children in the NW group preserved a more consistent alpha diversity of virulence factors, while OWOB microbiomes exhibited a dominance of virulence factors.

Differences in the metabolic capacities pertaining to biosynthesis pathways of vitamins, carriers, amino acids, nucleotides, nucleosides, amines, and polyamines, as well as the degradation of nucleotides, nucleosides, and carbohydrate-sugars, were also found between the NW and OWOB groups.


Dietary profiles and the diversity of gut microbiota were found to be interconnected and associated with changes in metabolic parameters, the dominance of virulence factors, and obesity. Changes in gut microbiome diversity and relative abundance have been linked to obesity, inflammatory responses, and metabolic disorders.

Taken together, the study findings suggested that the prevalence of virulence factors, as well as the metabolic and genetic roles of gut microbiota in increasing inflammation, can help identify individuals at an increased risk of childhood obesity.

Journal reference:
  • Murga-Garrido, S. M., Ulloa-Pérez, E. J., Díaz-Benítez, C. E., et al. (2023). Virulence factors of the gut microbiome are associated with BMI and metabolic blood parameters in children with obesity. Microbiology Spectrum. doi:10.1128/spectrum.03382-22

Duke researchers find human DNA sequence divergence after split from common ancestor of chimpanzees

A team of Duke researchers has identified a group of human DNA sequences driving changes in brain development, digestion and immunity that seem to have evolved rapidly after our family line split from that of the chimpanzees, but before we split with the Neanderthals.

Our brains are bigger, and are guts are shorter than our ape peers.

A lot of the traits that we think of as uniquely human, and human-specific, probably appear during that time period in the 7.5 million years since the split with the common ancestor we share with the chimpanzee.”

Craig Lowe, Ph.D., assistant professor of molecular genetics and microbiology in the Duke School of Medicine

Specifically, the DNA sequences in question, which the researchers have dubbed Human Ancestor Quickly Evolved Regions (HAQERS), pronounced like hackers, regulate genes. They are the switches that tell nearby genes when to turn on and off. The findings appear Nov.23 in the journal CELL.

The rapid evolution of these regions of the genome seems to have served as a fine-tuning of regulatory control, Lowe said. More switches were added to the human operating system as sequences developed into regulatory regions, and they were more finely tuned to adapt to environmental or developmental cues. By and large, those changes were advantageous to our species.

“They seem especially specific in causing genes to turn on, we think just in certain cell types at certain times of development, or even genes that turn on when the environment changes in some way,” Lowe said.

A lot of this genomic innovation was found in brain development and the GI tract. “We see lots of regulatory elements that are turning on in these tissues,” Lowe said. “These are the tissues where humans are refining which genes are expressed and at what level.”

Today, our brains are larger than other apes, and our guts are shorter. “People have hypothesized that those two are even linked, because they are two really expensive metabolic tissues to have around,” Lowe said. “I think what we’re seeing is that there wasn’t really one mutation that gave you a large brain and one mutation that really struck the gut, it was probably many of these small changes over time.”

To produce the new findings, Lowe’s lab collaborated with Duke colleagues Tim Reddy, an associate professor of biostatistics and bioinformatics, and Debra Silver, an associate professor of molecular genetics and microbiology to tap their expertise. Reddy’s lab is capable of looking at millions of genetic switches at once and Silver is watching switches in action in developing mouse brains.

“Our contribution was, if we could bring both of those technologies together, then we could look at hundreds of switches in this sort of complex developing tissue, which you can’t really get from a cell line,” Lowe said.

“We wanted to identify switches that were totally new in humans,” Lowe said. Computationally, they were able to infer what the human-chimp ancestor’s DNA would have been like, as well as the extinct Neanderthal and Denisovan lineages. The researchers were able to compare the genome sequences of these other post-chimpanzee relatives thanks to databases created from the pioneering work of 2022 Nobel laureate Svante Pääbo.

“So, we know the Neanderthal sequence, but let’s test that Neanderthal sequence and see if it can really turn on genes or not,” which they did dozens of times.

“And we showed that, whoa, this really is a switch that turns on and off genes,” Lowe said. “It was really fun to see that new gene regulation came from totally new switches, rather than just sort of rewiring switches that already existed.”

Along with the positive traits that HAQERs gave humans, they can also be implicated in some diseases.

Most of us have remarkably similar HAQER sequences, but there are some variances, “and we were able to show that those variants tend to correlate with certain diseases,” Lowe said, namely hypertension, neuroblastoma, unipolar depression, bipolar depression and schizophrenia. The mechanisms of action aren’t known yet, and more research will have to be done in these areas, Lowe said.

“Maybe human-specific diseases or human-specific susceptibilities to these diseases are going to be preferentially mapped back to these new genetic switches that only exist in humans,” Lowe said.

Journal reference:

Mangan, R.J., et al. (2022) Adaptive Sequence Divergence Forged New Neurodevelopmental Enhancers in Humans. Cell. doi.org/10.1016/j.cell.2022.10.016.

We’ve all seen the latest historical interpretations on television, the movies, or even the stage. And while talented …

We’ve all seen the latest historical interpretations on television, the movies, or even the stage. And while talented costumers, set producers, and makeup artists can work wonders in re-creating the past right down to unfortunate trends in premodern dental health, there’s something we don’t often see -or even think about- when it comes to human history: parasites.

Recently, the oldest known inscription (ever!) to use a phonetic alphabet was identified on a Canaanite comb from 4,000 years ago, The inscription reads, “May this tusk root out the lice of the hai[r and the] beard.” This find showcases what it meant -and still means- to be human, i.e., to live with parasites of all forms. 

Paleoparasitology is a specialized field within archaeology (and paleontology) that focuses on human-parasite relationships that have dominated our history and prehistory globally. The types of parasites that pester human populations differ from group to group -or population to population- depending on several factors like which environments we are living in, what animals we are interacting with, and how people interact with one another. The types of parasites that archaeologists can study also differ situationally, that is, depending on the preservation: i.e. mummified human remains vs. excavating a latrine or cesspool.

Apologies in advance if you feel itchy after reading.

Lice, Nits, and Otherwise Itchy Finds

4th c. Egyptian Comb. Digital image courtesy of the Getty's Open Content Program.In order to identify ectoparasites that live on humans, archaeologists need, well…humans. Or in some cases our clothing. Mummified human remains, particularly those with preserved hair or clothes are the best-case scenario when looking for prehistoric and historic ectoparasites.

Although eggs had been identified on both South American and Egyptian mummies prior to 1924, that was the year that the first adult lice were isolated and reported on from an Egyptian Mummy. Since then, nits, lice, and their eggs have been identified on mummies from various South American countries, Egypt, China, Greenland, and the Aleutian Islands (this is including both natural mummies and intentionally created mummies).

Lice have even been used to estimate when humans started to wear clothing by looking at when head lice evolved into body lice, approximately 70,000 to 170,000 years ago.

Our legacy with lice is a long one. Lice eggs collected from human remains in Brazil have been radiocarbon dated to 10,000 years ago. And while they didn’t have a special medicated soap to rid themselves of lice, special louse combs have been identified in Ancient Egyptian contexts from 6,500 years ago. Jumping to a little later in time, body lice eggs have also been found in 10th-14th century ‘Viking-Age’ Greenland.

And while head/body lice and nits are no fun for anyone, lets not forget the other sort of ectoparasite that’s followed humans around – Pthirus pubis L., or pubic lice- which have been found in Roman and medieval Britain.

Finally, and importantly, these parasites can spread more than just an itch, they can also spread disease. Lice and fleas in particular have been associated with several disease outbreaks in history. Most notably being the Bubonic Plague (associated with both fleas and lice), however molecular analysis has shown that louse-born infectious diseases played pivotal roles throughout history. For example B. quintana, which causes trench fever, “affected nearly one-third of Napoleon’s soldiers buried in Vilnius and indicate that these diseases might have been a major factor in the French retreat from Russia.”

Internal Irritations

Unfortunately for us, our external irritants are not the only parasites that have accompanied humans over time. Endoparasties, those that survive and reproduce inside of humans and animals, can also be identified by archaeologists.

The first endoparasite identified within mummified human remains was by Sir Marc Armand Ruffer in 1910. What he found were the calcified eggs of Schistosoma haematobium, the cause of schistosomiasis, in the preserved kidney of an Egyptian mummy dating to 3200 BCE. Today, the prevalence of schistosomiasis as a parasitic disease is second only to malaria worldwide.

Above Image: Life cycle of flatworms of the genus Schistosoma. Image Credit: CDC

More recently, Dr. Piers D. Mitchell and his colleagues, have reported on intestinal parasites identified at archaeological sites in the Mediterranean without having mummies. How did they do this you ask? Latrines.

Medieval manuscript illustration 14th-15th c. Digital image courtesy of the Getty's Open Content Program.Intestinal parasites like those reported on at these latrine sites, have complex life cycles that can be summarized as: growth, reproduction, and transmission. For the most part, it is the transmission phase that is identified archaeologically with latrines, i.e. eggs of these parasites identified in the soil that used to be an ancient or medieval latrine.

At a crusader-period site in modern Israel, roundworm (Ascaris lumbricoides) and fish tapeworm (Diphyllobothrium latum) were identified in latrine soils. This is particularly interesting given that this type of fish tapeworm was extremely uncommon in the eastern Mediterranean at the time. It was, however, very common in northern Europe. This case, as well as a recent case of ectoparasite DNA extraction, shows how regional parasites can spread with human migration and how we may be able to track prehistoric and historic human migration events and patterns using parasites.

However, it is also possible to find parasite eggs in other contexts. They have, so far, been identified in coprolites (preserved fecal matter), or even in soil samples taken from non-mummified human burials in the area that was the digestive system. Some parasites, like Echinococcus granulosus (causes Hydatid disease), can create calcified cysts in the human liver and lungs, that, given fantastic preservation, can also be identified in skeletonized inhumation burials (non-mummified). These cysts have been found in medieval Iceland and were likely accidentally spread to humans from domesticated animals.

While there is so much more to say about parasites and what we can learn from them throughout human history and prehistory, let’s leave it at this, the next time you sit back to watch your favorite historical drama remember, almost everyone was probably just really itchy.


Sources: International Journal of Paleopathology (1), International Journal of Paleopathology (2), Science, Microbiology Spectrum, Trends in Parasitology, Journal of Egyptian Archaeology, Journal of Medical Entomology, Antiquity, ScienceDirect, The Lancet, The Journal of Infectious Diseases, Advances in Parasitology: Fossil Parasites, CDC, Britannica, International Journal of Osteoarchaeology, Nature, EurekaAlert!, Jerusalem Journal of Archaeology, Science News

Sarah Hoffman