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Microbial Cross-Feeding Scores Uncover Interactions That Influence Gut Health

The team developed a computational metabolite exchange scoring system to identify microbial cross feeding relationships–the use of metabolites produced…

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5 months ago

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An international research team led by scientists at the Hudson Institute of Medical Research has found a way to determine which species of gut microbiota are important in certain diseases, and how they interact with other microorganisms to create a healthy microbiome.

The team developed a computational metabolite exchange scoring system to identify microbial cross feeding relationships—the use of metabolites produced by one microorganism as an essential nutrients by another—and how these may be altered in disease. The researchers suggest that understanding such relationships could point to therapeutic approaches for a range of disorders including inflammatory bowel disease, infections, autoimmune diseases and cancer.

“There are roughly 1000 different bacterial species in a healthy gut—it’s a microscopic multicultural community with over a trillion individual members,” said research lead Samuel Forster, PhD. “Bacteria in our microbiomes exist as communities that rely on each other to produce and share key nutrients between them … We have developed a new computational way to understand these dependencies and their role in shaping our microbiome. This new method unlocks our understanding of the gut microbiome and provides a foundation for new treatment options that selectively remodel microbial communities.”

Associate Professor Samuel Forster from Hudson Institute of Medical Research is developing new ways of understanding interactions within the human gut microbiome. [Hudson Institute of Medical Research]
Forster’s team, working with collaborators at the Institute for Systems Biology, and at Monash University and Monash Health, reported their findings in Nature Communications, in a paper titled “Disease-specific loss of microbial cross-feeding interactions in the human gut.” In their paper the team concluded, “We propose that our conceptual framework will help prioritize in-depth analyses, experiments and clinical targets, and that targeting the restoration of microbial cross-feeding

interactions is a promising mechanism-informed strategy to reconstruct a healthy gut ecosystem … We show that our analytical framework identifies both known and novel microbiome-disease associations, providing a cost-efficient and mechanistically grounded strategy to prioritize experiments and guide clinical trials.”

The human gut contains hundreds of microbial species forming a complex and interdependent metabolic network, the authors explained. And more than half of the metabolites consumed by gut microbes are by-products of microbial metabolism, with the waste of one species serving as nutrients for other. This means that the loss of one species may impact on the survival or extinction of others. “Species interdependence can render microorganisms vulnerable to local extinction if a partner is lost unless alternative species are available to fill that niche,” the team continued. “Many gut microorganisms critical to human health rely on nutrients produced by each other for survival; however, these cross-feeding interactions are still challenging to quantify and remain poorly characterized.”

Forster and colleagues have spent years studying the gut microbiome and working out which species perform which functions. To help understand the link between cross-feeding interactions and disease, the team developed a computational metabolite exchange score (MES) that can quantify microbiome interactions. The system is designed to identify those microbial cross-feeding interactions that are most affected in disease. “MES is the product of the diversity of taxa predicted to consume and taxa predicted to produce a given metabolite, normalized by the total number of involved taxa,” the authors noted.

For their reported study, and to obtain an overview of the association between cross-feeding interactions and different diseases, the team applied the MES technique to exiting datasets. “To obtain an overview of the association between cross-feeding interactions and different diseases, we performed a large-scale analysis of 1661 high-quality and deeply sequenced gut metagenome samples, including 871 healthy and 790 diseased individuals from 33 published studies, 15 countries and 11 disease phenotypes,” they wrote. Using the MES platform the team was able to identify and rank metabolic interactions that were significantly affected by loss of cross-feeding partners in 10 out of 11 diseases.

For example, hydrogen sulphide was highlighted as a key factor in Crohn’s disease (CD). The investigators discovered that the association may relate to loss of bacteria that use hydrogen sulphide, H2S, not an increase in those species producing it, as was previously believed. “Our results suggest that CD patients lack microbial community members to support a healthy H2S balance,” they wrote. The study in addition identified other associations between the microbiome interactions and disease, including some that hadn’t previously been known.

“Our framework identified both known and novel microbiome-disease associations, including a link between colorectal cancer and the microbial metabolism of ethanol, a connection between rheumatoid arthritis with microbially-derived ribosyl nicotinamide, and links between Crohn’s disease and specific bacteria that metabolize hydrogen sulfide,” the investigators further noted. “… we found that H2S—a gas previously implicated in CD and IBD symptoms—was the metabolite most affected by the loss of cross-feeding microbial partners … .”

First author Vanessa Marcelino, PhD, says the new computational method for studying microbial communities was key to establishing the relationships. “This is a significant step in the development of complex microbial therapies. This approach allows us to identify and rank the key interactions between bacteria and use this knowledge to predict targeted ways to change the community.”

Forster and team have a long-standing relationship with Adelaide-based biotechnology company BiomeBank, which is working on new ways to treat and prevent disease by restoring gut microbial ecology. He commented, “Through the partnership between the Hudson Institute of Medical Research and BiomeBank, these insights into community structure will provide the opportunity for targeted intervention with rationally selected combinations of microbes,” Forster said. In their paper the team concluded, “We expect that metagenome-informed metabolic models, coupled with an assessment of microbial cross-feeding interactions, will help alleviate one of the main barriers in the development of microbiome therapies—prioritizing which species or metabolites to target. By focusing on restoring key aspects of the gut ecology, we may be able to introduce more effective and long-lasting changes in the human gut microbiome.”

The post Microbial Cross-Feeding Scores Uncover Interactions That Influence Gut Health appeared first on GEN - Genetic Engineering and Biotechnology News.

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February Employment Situation

By Paul Gomme and Peter Rupert The establishment data from the BLS showed a 275,000 increase in payroll employment for February, outpacing the 230,000…

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18 hours ago

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March 9, 2024

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By Paul Gomme and Peter Rupert

The establishment data from the BLS showed a 275,000 increase in payroll employment for February, outpacing the 230,000 average over the previous 12 months. The payroll data for January and December were revised down by a total of 167,000. The private sector added 223,000 new jobs, the largest gain since May of last year.

Temporary help services employment continues a steep decline after a sharp post-pandemic rise.

Average hours of work increased from 34.2 to 34.3. The increase, along with the 223,000 private employment increase led to a hefty increase in total hours of 5.6% at an annualized rate, also the largest increase since May of last year.

The establishment report, once again, beat “expectations;” the WSJ survey of economists was 198,000. Other than the downward revisions, mentioned above, another bit of negative news was a smallish increase in wage growth, from $34.52 to $34.57.

The household survey shows that the labor force increased 150,000, a drop in employment of 184,000 and an increase in the number of unemployed persons of 334,000. The labor force participation rate held steady at 62.5, the employment to population ratio decreased from 60.2 to 60.1 and the unemployment rate increased from 3.66 to 3.86. Remember that the unemployment rate is the number of unemployed relative to the labor force (the number employed plus the number unemployed). Consequently, the unemployment rate can go up if the number of unemployed rises holding fixed the labor force, or if the labor force shrinks holding the number unemployed unchanged. An increase in the unemployment rate is not necessarily a bad thing: it may reflect a strong labor market drawing “marginally attached” individuals from outside the labor force. Indeed, there was a 96,000 decline in those workers.

Earlier in the week, the BLS announced JOLTS (Job Openings and Labor Turnover Survey) data for January. There isn’t much to report here as the job openings changed little at 8.9 million, the number of hires and total separations were little changed at 5.7 million and 5.3 million, respectively.

As has been the case for the last couple of years, the number of job openings remains higher than the number of unemployed persons.

Also earlier in the week the BLS announced that productivity increased 3.2% in the 4th quarter with output rising 3.5% and hours of work rising 0.3%.

The bottom line is that the labor market continues its surprisingly (to some) strong performance, once again proving stronger than many had expected. This strength makes it difficult to justify any interest rate cuts soon, particularly given the recent inflation spike.

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Mortgage rates fall as labor market normalizes

Jobless claims show an expanding economy. We will only be in a recession once jobless claims exceed 323,000 on a four-week moving average.

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1 day ago

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March 8, 2024

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Everyone was waiting to see if this week’s jobs report would send mortgage rates higher, which is what happened last month. Instead, the 10-year yield had a muted response after the headline number beat estimates, but we have negative job revisions from previous months. The Federal Reserve’s fear of wage growth spiraling out of control hasn’t materialized for over two years now and the unemployment rate ticked up to 3.9%. For now, we can say the labor market isn’t tight anymore, but it’s also not breaking.

The key labor data line in this expansion is the weekly jobless claims report. Jobless claims show an expanding economy that has not lost jobs yet. We will only be in a recession once jobless claims exceed 323,000 on a four-week moving average.

From the Fed: In the week ended March 2, initial claims for unemployment insurance benefits were flat, at 217,000. The four-week moving average declined slightly by 750, to 212,250


Below is an explanation of how we got here with the labor market, which all started during COVID-19.

1. I wrote the COVID-19 recovery model on April 7, 2020, and retired it on Dec. 9, 2020. By that time, the upfront recovery phase was done, and I needed to model out when we would get the jobs lost back.

2. Early in the labor market recovery, when we saw weaker job reports, I doubled and tripled down on my assertion that job openings would get to 10 million in this recovery. Job openings rose as high as to 12 million and are currently over 9 million. Even with the massive miss on a job report in May 2021, I didn’t waver.

Currently, the jobs openings, quit percentage and hires data are below pre-COVID-19 levels, which means the labor market isn’t as tight as it once was, and this is why the employment cost index has been slowing data to move along the quits percentage.  

2-US_Job_Quits_Rate-1-2

3. I wrote that we should get back all the jobs lost to COVID-19 by September of 2022. At the time this would be a speedy labor market recovery, and it happened on schedule, too

Total employment data

4. This is the key one for right now: If COVID-19 hadn’t happened, we would have between 157 million and 159 million jobs today, which would have been in line with the job growth rate in February 2020. Today, we are at 157,808,000. This is important because job growth should be cooling down now. We are more in line with where the labor market should be when averaging 140K-165K monthly. So for now, the fact that we aren’t trending between 140K-165K means we still have a bit more recovery kick left before we get down to those levels. 




From BLS: Total nonfarm payroll employment rose by 275,000 in February, and the unemployment rate increased to 3.9 percent, the U.S. Bureau of Labor Statistics reported today. Job gains occurred in health care, in government, in food services and drinking places, in social assistance, and in transportation and warehousing.

Here are the jobs that were created and lost in the previous month:

IMG_5092

In this jobs report, the unemployment rate for education levels looks like this:

  • Less than a high school diploma: 6.1%
  • High school graduate and no college: 4.2%
  • Some college or associate degree: 3.1%
  • Bachelor’s degree or higher: 2.2%
IMG_5093_320f22

Today’s report has continued the trend of the labor data beating my expectations, only because I am looking for the jobs data to slow down to a level of 140K-165K, which hasn’t happened yet. I wouldn’t categorize the labor market as being tight anymore because of the quits ratio and the hires data in the job openings report. This also shows itself in the employment cost index as well. These are key data lines for the Fed and the reason we are going to see three rate cuts this year.

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Inside The Most Ridiculous Jobs Report In History: Record 1.2 Million Immigrant Jobs Added In One Month

Inside The Most Ridiculous Jobs Report In History: Record 1.2 Million Immigrant Jobs Added In One Month

Last month we though that the January…

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March 8, 2024

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Inside The Most Ridiculous Jobs Report In History: Record 1.2 Million Immigrant Jobs Added In One Month

Last month we though that the January jobs report was the "most ridiculous in recent history" but, boy, were we wrong because this morning the Biden department of goalseeked propaganda (aka BLS) published the February jobs report, and holy crap was that something else. Even Goebbels would blush. 

What happened? Let's take a closer look.

On the surface, it was (almost) another blockbuster jobs report, certainly one which nobody expected, or rather just one bank out of 76 expected. Starting at the top, the BLS reported that in February the US unexpectedly added 275K jobs, with just one research analyst (from Dai-Ichi Research) expecting a higher number.

Some context: after last month's record 4-sigma beat, today's print was "only" 3 sigma higher than estimates. Needless to say, two multiple sigma beats in a row used to only happen in the USSR... and now in the US, apparently.

Before we go any further, a quick note on what last month we said was "the most ridiculous jobs report in recent history": it appears the BLS read our comments and decided to stop beclowing itself. It did that by slashing last month's ridiculous print by over a third, and revising what was originally reported as a massive 353K beat to just 229K,  a 124K revision, which was the biggest one-month negative revision in two years!

Of course, that does not mean that this month's jobs print won't be revised lower: it will be, and not just that month but every other month until the November election because that's the only tool left in the Biden admin's box: pretend the economic and jobs are strong, then revise them sharply lower the next month, something we pointed out first last summer and which has not failed to disappoint once.

To be fair, not every aspect of the jobs report was stellar (after all, the BLS had to give it some vague credibility). Take the unemployment rate, after flatlining between 3.4% and 3.8% for two years - and thus denying expectations from Sahm's Rule that a recession may have already started - in February the unemployment rate unexpectedly jumped to 3.9%, the highest since February 2022 (with Black unemployment spiking by 0.3% to 5.6%, an indicator which the Biden admin will quickly slam as widespread economic racism or something).

And then there were average hourly earnings, which after surging 0.6% MoM in January (since revised to 0.5%) and spooking markets that wage growth is so hot, the Fed will have no choice but to delay cuts, in February the number tumbled to just 0.1%, the lowest in two years...

... for one simple reason: last month's average wage surge had nothing to do with actual wages, and everything to do with the BLS estimate of hours worked (which is the denominator in the average wage calculation) which last month tumbled to just 34.1 (we were led to believe) the lowest since the covid pandemic...

... but has since been revised higher while the February print rose even more, to 34.3, hence why the latest average wage data was once again a product not of wages going up, but of how long Americans worked in any weekly period, in this case higher from 34.1 to 34.3, an increase which has a major impact on the average calculation.

While the above data points were examples of some latent weakness in the latest report, perhaps meant to give it a sheen of veracity, it was everything else in the report that was a problem starting with the BLS's latest choice of seasonal adjustments (after last month's wholesale revision), which have gone from merely laughable to full clownshow, as the following comparison between the monthly change in BLS and ADP payrolls shows. The trend is clear: the Biden admin numbers are now clearly rising even as the impartial ADP (which directly logs employment numbers at the company level and is far more accurate), shows an accelerating slowdown.

But it's more than just the Biden admin hanging its "success" on seasonal adjustments: when one digs deeper inside the jobs report, all sorts of ugly things emerge... such as the growing unprecedented divergence between the Establishment (payrolls) survey and much more accurate Household (actual employment) survey. To wit, while in January the BLS claims 275K payrolls were added, the Household survey found that the number of actually employed workers dropped for the third straight month (and 4 in the past 5), this time by 184K (from 161.152K to 160.968K).

This means that while the Payrolls series hits new all time highs every month since December 2020 (when according to the BLS the US had its last month of payrolls losses), the level of Employment has not budged in the past year. Worse, as shown in the chart below, such a gaping divergence has opened between the two series in the past 4 years, that the number of Employed workers would need to soar by 9 million (!) to catch up to what Payrolls claims is the employment situation.

There's more: shifting from a quantitative to a qualitative assessment, reveals just how ugly the composition of "new jobs" has been. Consider this: the BLS reports that in February 2024, the US had 132.9 million full-time jobs and 27.9 million part-time jobs. Well, that's great... until you look back one year and find that in February 2023 the US had 133.2 million full-time jobs, or more than it does one year later! And yes, all the job growth since then has been in part-time jobs, which have increased by 921K since February 2023 (from 27.020 million to 27.941 million).

Here is a summary of the labor composition in the past year: all the new jobs have been part-time jobs!

But wait there's even more, because now that the primary season is over and we enter the heart of election season and political talking points will be thrown around left and right, especially in the context of the immigration crisis created intentionally by the Biden administration which is hoping to import millions of new Democratic voters (maybe the US can hold the presidential election in Honduras or Guatemala, after all it is their citizens that will be illegally casting the key votes in November), what we find is that in February, the number of native-born workers tumbled again, sliding by a massive 560K to just 129.807 million. Add to this the December data, and we get a near-record 2.4 million plunge in native-born workers in just the past 3 months (only the covid crash was worse)!

The offset? A record 1.2 million foreign-born (read immigrants, both legal and illegal but mostly illegal) workers added in February!

Said otherwise, not only has all job creation in the past 6 years has been exclusively for foreign-born workers...

Source: St Louis Fed FRED Native Born and Foreign Born

... but there has been zero job-creation for native born workers since June 2018!

This is a huge issue - especially at a time of an illegal alien flood at the southwest border...

... and is about to become a huge political scandal, because once the inevitable recession finally hits, there will be millions of furious unemployed Americans demanding a more accurate explanation for what happened - i.e., the illegal immigration floodgates that were opened by the Biden admin.

Which is also why Biden's handlers will do everything in their power to insure there is no official recession before November... and why after the election is over, all economic hell will finally break loose. Until then, however, expect the jobs numbers to get even more ridiculous.

Tyler Durden Fri, 03/08/2024 - 13:30

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