Rosa Rubicondior: Creationism Refuted - Why We Need Our Gut Microbiome To Keep Us Healthy

Electron microscopic image of rod-shaped gut bacteria.

What gut bacteria like

An open access paper in Proceedings of the National Academy of Sciences of the USA (PNAS) is a stunning example of the ludicrous complexity evolution has produced — the exact antithesis of what an intelligent designer would create, if such a designer were anything more than grossly incompetent. As I explain in my book, The Unintelligent Designer: Refuting The Intelligent Design Hoax, and as I have pointed out repeatedly on this blog, the hallmark of intelligent design should be minimal complexity and maximal efficiency. And yet what we find in humans — and in just about every other bilaterian animal with a gut — is a vast, intricate symbiotic microbiome supplying functions that could far more simply have been provided directly, with even a little forethought on the part of any competent designer.

Instead, in the sort of convoluted complexity that creationists like to attribute to their putative designer god, but which is in reality a hallmark of evolved systems, we see yet another example of a biological arrangement that betrays not intelligence, but its absence.

The paper, by an international team led by Professor Victor Sourjik and colleagues from the Max Planck Institute for Terrestrial Microbiology, the University of Ohio, and Philipps-University Marburg, describes how an interdependent gut microbiome helps to keep both the microorganisms and their host healthy. They show that this complex and dynamic community is governed by countless chemical interactions — not only among the microorganisms themselves, but also between microbes and host tissues. The perception of nutrients and signalling molecules by gut bacteria is therefore crucial in maintaining these relationships.

One key role of this microbiome is in deterring and combating pathological species which would otherwise find the gut — with its warmth and steady supply of pre-digested nutrients — an ideal environment to colonise. This must have been a problem even for the earliest animals with a digestive tract: a vulnerability effectively built into the body plan. The solution, in the form of beneficial commensal organisms, is therefore probably as old as the first tube-like bilaterians themselves.

The problem the human gut faces in this respect can be gauged from the fact that some studies have shown that 50-55% or more of the dry weight of human faces is bacteria, dead and alive[1] , with populations of bacteria in the order of 10¹¹ bacteria per gram![2] Imagine then the opportunities this presents to a potentially pathological bacteria with a generation time in minutes. With a population exploding exponentially, the potential to overwhelm the host in a few days is enormous. This is the scale of the problem, and of the selection pressure to overcome it, that has produced this massively complex solution, because it wasn't solved in the initial 'design' stage.

Since it worked well enough, there has been no evolutionary pressure to replace it with a less vulnerable gut, or one better equipped to cope with infection without relying on an entire ecosystem of different microorganisms to maintain health. In other words, what we have today is the result of more than half a billion years of evolutionary history since this basic body plan first emerged in the Cambrian.

Background^ The Ancient Evolutionary Origins of the Gut Microbiome. One of the most striking features of animal life is that very few animals are truly “individuals” in the simple sense creationists imagine. In reality, most animals — including humans — are better understood as ecosystems, hosting vast communities of microorganisms that are essential to survival.

The origin of this relationship is probably extremely ancient.

The first animals with a tube-like digestive tract appeared in the early Cambrian, more than 520 million years ago, among the earliest bilaterians — animals with a mouth, an intestine, and an anus. This new body plan brought major advantages: food could be processed continuously, nutrients absorbed efficiently, and waste eliminated separately.

But it also created an evolutionary problem.

A moist intestine filled with nutrient-rich material is an ideal habitat not only for digestion, but also for invading pathogens. The gut is effectively an open doorway into the body, and it would have been vulnerable from the moment it evolved.

The evolutionary solution was not the creation of a perfectly sealed or self-sterilising digestive system, but something far more typical of evolution: a patchwork alliance.

Beneficial microorganisms colonised the gut and formed stable communities that could:

outcompete harmful invaders
help digest otherwise inaccessible nutrients
produce essential vitamins and metabolites
interact with the immune system
regulate inflammation and gut development

In return, the microbes gained a protected environment and a steady food supply.

This kind of symbiosis is now so deeply embedded in animal biology that many species cannot develop normally without their microbial partners. The immune system itself has evolved in constant dialogue with these organisms, learning to tolerate helpful species while resisting dangerous ones.

Far from being an elegant design, the gut microbiome is an example of evolutionary history written into physiology: a complex, interdependent compromise shaped by natural selection over hundreds of millions of years.

It is not what an engineer would build from scratch.

It is exactly what evolution produces: systems that work well enough, because they were never planned — only inherited.

This research, and its significance for understanding the intricate interactions between gut organisms and their hosts, is explained for a lay audience in a news item from the Max Planck Institute.

What gut bacteria like
The sensory abilities of bacteria in the gut are both precise and evolutionarily adaptable
To the point

Chemical signals: Receptors that have been little researched to date could play an important role in the search for nutrients by beneficial, motile bacteria in the intestine and in communication between bacteria and the host.
Significance: The research strategy expands knowledge about the sensory abilities of beneficial intestinal bacteria and can also be transferred to other microbial ecosystems in the future.

The gut microbiome, also known as the gut flora, is essential for health. This complex and dynamic community of microorganisms is governed by numerous chemical interactions between the microorganisms themselves and with their host. The perception of nutrients and signaling molecules by gut bacteria is thus crucial for these interactions, yet the wide repertoire of signals recognized by bacterial receptors remains largely unknown.

Which signals are relevant for beneficial gut bacteria?

Research on the sensory abilities of bacteria has so far mainly focused on model organisms, particularly pathogens. But what signals do the sensors of so-called commensals, non-pathogenic or even beneficial bacteria that live in humans, ‘read’?

An international team led by Victor Sourjik, which included researchers from the Max Planck Institute for Terrestrial Microbiology, the University of Ohio and the Philipps-University Marburg, has now shown that commensal bacteria can perceive and respond to diverse chemical stimuli in their environment. They focused on Clostridia, motile bacteria that are present in large numbers in the intestinal flora and play an important role in maintaining gut health.

The researchers discovered that the receptors derived from the human gut microbiome recognize a surprisingly broad spectrum of metabolic substances. These include the breakdown products of carbohydrates, fats, proteins, DNA, and amines. Systematic screening revealed clear preferences for particular classes of chemicals, which differ between types of the bacterial sensors.

Lactate and formate: Important metabolites for gut bacteria

Using a combination of experimental and bioinformatic methods, the researchers identified multiple specific chemical ligands for sensory receptors that control the movement of motile bacteria. They observed that these sensors are used by bacteria to detect nutritionally valuable chemicals, suggesting that finding sources of nutrients is the key function of motility in these bacteria. Their results showed that lactic acid (lactate) and formic acid (formate) are the most common stimuli and may thus serve as particularly important nutrients for bacterial growth in the gut.

The fact that these compounds can also be produced by some gut bacteria underlines the significance of 'cross-feeding', a process where one bacterial species releases metabolites that feed other species.

These domains appear to be important for interactions between bacteria in the gut and could play a key role in the healthy human microbiome.

Dr. Wenhao Xu, first author.
Max Planck Institute for Terrestrial Microbiology
Marburg, Germany.

The discovery of sensors with novel specificities

By systematically assessing specificities of multiple sensors, the researchers discovered several previously unknown groups of sensory domains specific for lactate, dicarboxylic acids, uracil (a RNA building block) and short-chain fatty acids (SCFAs).

They also succeeded in elucidating the crystal structure of a novel dual sensor of uracil and acetate with its ligands, thereby deciphering their binding mechanism. This sensor belongs to a large class of sensory domains with diverse specificities, and the analysis of the evolutionary relationship between uracil sensors and other sensors belonging to this class revealed remarkable ease with which their ligand specificity changes over the course of evolution. This highlights the adaptability of sensory receptors in response to changes in the bacterial environmental niche.

Our research project has significantly expanded the understanding of sensory abilities of beneficial gut bacteria. To our knowledge, this is the first systematic analysis of the sensory preferences of non-model bacteria that colonise a specific ecological niche. Looking ahead, our approach can be similarly applied to systematically investigate sensory preferences in other microbial ecosystems.

Professor Victor Sourjik, Senior author
Max Planck Institute for Terrestrial Microbiology
Marburg, Germany.

Publication:
W. Xu, E. Jalomo-Khayrova, V.M. Gumerov, P.A. Ross, T.S. Köbel, D. Schindler, G. Bange, I.B. Zhulin, & V. Sourjik (2025)
Specificities of chemosensory receptors in the human gut microbiota
Proc. Natl. Acad. Sci. U.S.A. 122(35) e2508950122, https://doi.org/10.1073/pnas.2508950122.

Significance
Environmental sensing is highly important for bacterial growth and survival in diverse habitats, but the sensory repertoire of bacterial receptors remains largely uncharacterized. While most previous studies have focused on individual model organisms, here we took a habitat-centric approach, systematically identifying chemically diverse ligands of selected Cache-type domains from a set of nonmodel bacteria inhabiting a particular ecological niche, the human gut. Our analyses provided important insights into the sensory and metabolic preferences of motile commensal bacteria in the human gut microbiota, indicating the prevalence of cross-feeding mediated by short-chain carboxylic acids. Furthermore, we biochemically and structurally characterized several specificities of Cache domains and demonstrated a surprisingly high evolvability of these sensors toward metabolites relevant to the gut microbiota.

Abstract
The human gut is rich in metabolites and harbors a complex microbial community, yet surprisingly little is known about the spectrum of chemical signals detected by the large variety of sensory receptors present in the gut microbiome. Here, we systematically mapped the ligand specificities of selected extracytoplasmic sensory domains from twenty members of the human gut microbiota, with a primary focus on the abundant and physiologically important class of Clostridia. Twenty-five metabolites from different chemical classes—including amino acids, nucleobase derivatives, amines, indole, and carboxylates—were identified as specific ligands for fifteen sensory domains from nine bacterial species, which represent all three major functional classes of transmembrane receptors: chemotaxis receptors, histidine kinases, and enzymatic sensors. We have further characterized the specificity and evolution of ligand binding to Cache superfamily sensors specific for lactate, dicarboxylic acids, and for uracil and short-chain fatty acids (SCFAs). Structural and biochemical analysis of the dCache sensor of uracil and SCFAs revealed that its two different ligand types bind at distinct sensory modules. Overall, combining experimental identification with computational analyses, we were able to assign ligands to approximately half of the Cache-type chemotaxis receptors found in the eleven gut commensal genomes from our set, with carboxylic acids representing the largest ligand class. Among these, the most commonly found ligand specificities were for lactate and formate, indicating a particular importance of these metabolites in the human gut microbiota and consistent with their observed growth-promoting effects on selected bacterial commensals.

And so, once again, reality refuses to cooperate with creationist expectations. The gut microbiome is not a decorative flourish on an otherwise pristine design; it is an essential, ancient, and deeply contingent biological compromise. It exists because a tube-like digestive tract is, by its very nature, an open invitation to microbial colonisation. The “solution” is not elegant engineering but evolutionary pragmatism: fill the vulnerable space with allies before enemies arrive.

Indeed, the sheer scale of microbial life in the intestine makes the point almost absurdly clear. Roughly half the dry weight of human faeces consists of bacteria — the remains of organisms that have replicated in staggering numbers inside us. This is not the hallmark of foresight. It is what happens when evolution builds systems that are good enough to persist, not perfect enough to impress an engineer.

Creationists, of course, will insist that this intricate interdependence is evidence of design. But that simply raises the obvious question: why design an animal that cannot digest properly, regulate immunity, or resist infection without outsourcing so much of its basic physiology to an entire ecosystem of microbes? Why construct a digestive tract that is, in effect, a permanently inhabited petri dish?

The answer is the one Intelligent Design advocates will never accept: because no one designed it. This is not the work of a competent architect, but the product of natural selection tinkering with inherited vulnerabilities over hundreds of millions of years. The gut microbiome is not a signature of intelligence. It is a signature of history.

Evolution explains it effortlessly. Intelligent Design can only gesture at it, then quietly look away.

What we see in the gut is not the fingerprint of a designer, but the footprints of half a billion years of evolutionary improvisation.

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