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Original story from the University of Illinois Urbana-Champaign (IL, USA).

Method used to screen and prepare metagenomic libraries for the presence of antibiotic resistance genes in tiny environmental samples.

Scientists from the University of Illinois Urbana-Champaign College of Agricultural, Consumer and Environmental Sciences (IL, USA) have developed a method to isolate genes from amounts of microbial DNA so tiny that it would take 20,000 samples to weigh as much as a single grain of sugar. In a recent paper, researchers discovered previously unknown antibiotic resistance genes in bacterial DNA isolated from human stool and from fish tanks at Chicago’s Shedd Aquarium (IL, USA).

“With antibiotic resistance on the rise, it’s more important than ever to understand the full diversity of mechanisms bacteria may be using to inactivate or avoid antibiotics,” commented senior author Terence Crofts. “If we can get a clearer view of the antibiotic resistance genes that exist out in the environment, that will give biomedical researchers a chance to look out for them in the clinic and potentially design more effective drugs.”

Crofts previously developed the method, known as METa assembly, to improve a microbiology tool known as a functional metagenomic library, which enables researchers to capture bacterial genes from the environment. The method allows researchers to collect soil, stool or other environmental samples and screen for the presence of potentially new microbial genes without having to culture the microbes or sequence their genomes. What’s more, METa assembly requires 100 times less DNA than standard functional metagenomic libraries, which is useful where microbes are scarce or when researchers can’t take large samples.

“We used to take the DNA out of the bacteria and just sequence it, but there are so many new genes in those environments that our sequencing ability has far outstripped our ability to actually guess at the functions of those genes,” Crofts explained. “A lot of these genes have unknown functions, so functional metagenomic screens are a way to get around that problem.”

Instead of sequencing the DNA, the researchers use an enzyme to chop it into gene-size pieces, which they then introduce to E. coli bacteria in the lab. E. coli, which is easier to grow in lab settings than many other microbes, incorporates the foreign DNA into its genetic machinery and begins to take on its traits. Crofts says antibiotic resistance traits are especially well-suited for study using functional metagenomic libraries because they’re usually controlled by a single gene, and it’s easy to tell whether bacteria have it or not.

“If E. coli has a resistance gene, it can survive an antibiotic. If it doesn’t, it dies,” he shared. “We might have 10 million E. coli cells in a petri dish with 10 million unique random chunks of environmental DNA. If we expose it to a particular antibiotic and only 10 colonies survive, we know those 10 had a resistance gene. Then it becomes very easy to take those colonies and sequence the chunk of DNA they grabbed from that environmental sample.”

Even if the sequencing result turns up genes for unknown proteins, the researchers know that they have a role in antibiotic resistance and can immediately drill down to study their mechanisms.

Crofts and his team tested the method on a sample of water from a large tank at Shedd Aquarium, where microbes are far less populous than in other environments like soil. They also tested a tiny sample from a product that usually teems with bacteria: human fecal matter.

“Because aquatic samples are usually less dense with microbes, you usually can’t get as much DNA out of them, but we showed that we could still make good libraries from the aquarium sample,” Crofts explained. “It’s also significant that we could make a functional metagenomic library from just a swab sample of fecal matter. That could be useful for clinical settings.”

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The team didn’t just make libraries from these samples, they made new discoveries about how microbes resist antibiotics. For example, in tetracycline-resistant sequences from Shedd Aquarium, the researchers identified new types of efflux pumps – protein channels that pump substances across the cell membrane – that remove tetracycline from cells.

Interestingly, some of the E. coli colonies from the human fecal sample resisted a group of antibiotics known as streptothricins. These were tested in the 1940s, but were never brought to market due to kidney toxicity in mammals. But with so much resistance in the current antibiotic landscape, Crofts says biomedical researchers are looking into streptothricin again (in less toxic forms).

“We found what looks like an entirely new family of streptothricin resistance proteins in our sequences,” he remarked. “Streptothricin is being brought up as this potentially clinically useful antibiotic, but we should really be trying to find out what resistance is already out there in the environment. And instead of making traditional streptothricins less toxic, maybe we should make a next-generation analog that can beat the antibiotic resistance mechanisms that may already exist in nature.”

Crofts plans to deploy his METa assembly method to agricultural systems – sampling soil and from ‘nose to tail’ in livestock – since antibiotic resistance not only occurs on the farm, it often originates on the farm.

“We produce a lot of antibiotics by culturing soil bacteria that make antibiotics as weapons to fight other bacteria. So, soils therefore have a very rich diversity of antibiotic resistance genes,” Crofts concluded. “Agriculture puts all these mammals in close association with this reservoir of antibiotic resistance genes in the soil. Since we’re giving these animals large amounts of antibiotics it becomes a very ripe environment for resistance to develop and jump into bacteria that can impact our own health.”

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Research on the microbes living in our digestive tract has triggered a ‘revolution’ in nutritional science.

In the last few years, dietary fiber has become the “new protein”, added to foods in abundance to feed our gut’s microbiome and boost our health.

However, a study on mice published in 2024 suggests that not all fiber supplements are equally beneficial.

Related: Eating Fiber Could Protect You From Infections. Here’s Why.

A form that is readily found in oats and barley, called beta-glucan, can control blood sugar and assist in weight loss among mice fed a high-fat diet.

Researchers at the University of Arizona (UA) and the University of Vienna found it decreased a mouse’s fat content and body weight within 18 weeks.

Other fibers they tested, including wheat dextrin, pectin, resistant starch, and cellulose, had no such effect, despite shifting the makeup of the mouse microbiome significantly compared to mice fed no fiber supplements.

“We know that fiber is important and beneficial; the problem is that there are so many different types,” explained biomedical scientist Frank Duca from UA in July last year.

“We wanted to know what kind of fiber would be most beneficial for weight loss and improvements in glucose homeostasis so that we can inform the community, the consumer, and then also inform the agricultural industry.”

Dietary fibers are the main source of energy for bacteria living in our guts, and yet less than 5 percent of people in the US consume the recommended 25–30 grams (0.9–1 ounce) of fiber a day.

To make up for this, fiber supplements and ‘invisible fiber’-infused foods are growing in popularity. But fibers are extremely diverse, so which do we choose?

Some fibers, like oat beta-glucans and wheat dextrin, are water-soluble, meaning they are easily fermented by gut bacteria.

Others, like cellulose and resistant starch, are less soluble or insoluble, meaning they stick to other materials to form stool.

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Until now, writes biomedical scientist Elizabeth Howard from UA and her colleagues, “there is no study that has investigated the role of various fibers in one cohort.”

To make up for this, the current study tested several forms of fiber in one cohort of mice. Only beta-glucan was found to increase the number of Ileibacterium in the mouse intestine. Other studies on mice have linked this bacterium to weight loss.

Sure enough, long before the 10-week marker, mice fed beta-glucan showed reduced body weight and body fat content compared to mice fed other forms of fiber.

The findings align with another recent study by Duca, which fed barley flour, rich in beta-glucan, to rodents. Even though the rats continued eating just as much of their high-fat diet as before, their energy expenditure increased and they lost weight anyway.

A similar outcome was observed in mice fed beta-glucan in the new study. These animals also showed increased concentrations of butyrate in their guts, which is a metabolite made when microbes break down fiber.

Butyrate induces the release of glucagon-like peptide-1 (GLP-1), which is the natural protein that synthetic drugs like Ozempic mimic to stimulate insulin release.

“Part of the benefits of consuming dietary fiber is through the release of GLP-1 and other gut peptides that regulate appetite and body weight,” said Duca.

“However, we don’t think that’s all of the effect. We think that there are other beneficial things that butyrate could be doing that are not gut peptide related, such as improving gut barrier health and targeting peripheral organs like the liver.”

Far more research is needed before these results can be extended to humans, but the findings suggest that some fibers may be better suited to weight loss and insulin control than others.

The study was published in the Journal of Nutrition.

An earlier version of this article was published in July 2024.

Vets are urging farmers to put in place mitigation strategies to curtail a surprising increase in respiratory disease linked to immunosuppression in young, suckled, grazing calves.

The rise in cases of classic pneumonia in suckled calves at grass in May, June and July has been significant, says Colin Mason, veterinary investigation officer at Scotland Rural College’s (SRUC) Disease Surveillance Centre, Dumfries.

See also: Advice on reducing pneumonia risk as autumn weather swings

“The thing that’s surprising is it’s occurring at a time when animals should be living their best life: they’re outside, suckling their dam’s milk, on good grass – especially in Scotland. They’re not wanting for anything.”

Unlike parasitic pneumonia associated with lungworm, which is often seen at grass in August and September, these cases are typically bacterial infections.

Colin explains that bacterial pneumonia is an “opportunist” that will take advantage of a compromised animal.

This is seen in the case data, with many individuals showing sign of predisposing factors that are potentially compromising immunity and acting as a gateway for respiratory issues.

The four main predisposing factors are:

1 Tick-borne disease

Colin estimates that 20% of cases of respiratory disease in first-grazing suckler calves could be tick related.

Tick-borne fever, for example, will compromise the immunity of infected cattle by negatively affecting white blood cells.

Tick-spread and tick-borne diseases are on the rise, making it an area for concern for all farmers, regardless of geography (see “Tick-borne disease on the up”).

Prevention involves avoiding ground with dense vegetation or long grass.

Licensed pour-on treatments can also be used, but options are limited and climate change and increased tick spread may mean a different approach is required in the future.

“We might have to think about how we breed cattle that are more resistant to ticks. We can’t be wholly reliant on chemicals to control the problem, we need to find sustainable solutions to cope,” he says.

2 Vitamin and trace element status

Vitamin E and selenium are important for immunity, particularly in fast-growing continental calves.

“Their requirements for vitamin E and selenium can be quite high to manage oxidative stress in growing muscles.

“It’s down to whether they’re getting sufficient,” Colin says.

More than half of all calves presented for post-mortem at SRUC Veterinary Services between 2016 and 2020 had signs of deficiency (see table), which could be compromising their immune status.

Colin urges farmers to ensure suckler cows are supplemented sufficiently, including during outwintering and after turnout, when it can be forgotten. That way, trace elements can be transmitted to calves via the dam’s milk.

Calves should be supplemented accordingly.

When calf pneumonia is a problem at grass, he suggests working with a vet to blood test six typical cows to establish selenium and vitamin E status.

Appropriate supplementation can then be planned and could involve boluses, supplementing dams or providing licks.

3 Bovine viral diarrhoea

Exposure to bovine viral diarrhoea (BVD) will have a negative impact on any animal’s ability to mount an effective immune response. The key is to work with a vet to understand a herd’s BVD status and design a herd-specific control strategy.

This should focus on routine testing, vaccination, and identifying and removing persistently infected animals, which act as the main route of infection.

4 Coccidiosis

Coccidiosis can cause acute, bloody scours or death, but more commonly can simply reduce calf resilience and act as a gateway disease for other problems.

“Very often, respiratory disease follows on from an episode of gut disease, so it’s always worth reviewing coccidiosis status as part of this,” Colin suggests.

This should involve working with a vet to identify risk factors, putting preventive strategies in place with a focus on exceptional hygiene, and targeting treatment as necessary.

In general, any unexplained calf deaths at about eight weeks old should also be investigated, to ensure any issues are addressed promptly.

“You’re not expecting calves to die at that stage, especially of respiratory disease, so [even] small levels [of mortality] are significant,” Colin emphasises.