Biology subjects

Gardner, A.

Publications and source records attributed to Gardner, A..

At least 19 recordsLinked to original sources

bioRxiv2026

AAV-NRF2 protects retinal and choroidal vasculature in a GDF15-dependent manner in an oxidative damage model of AMD

Oxidative stress is proposed to be a driver of age-related diseases. Age-related macular degeneration is one such disease, where the retinal pigment epithelium (RPE) is affected early in the disease. Vasculature damage also occurs, sometimes preceding RPE damage. To model some aspects of dry AMD, we used the NaIO3 mouse model of oxidative damage. Disruption of the deep retinal vascular plexus, disorganization and death of capillaries within the choriocapillaris, and marked electroretinographic decline were observed. AAV overexpressing the transcription factor, NRF2, which induces anti-oxidation enzymes and represses inflammation, was tested for protection of damage. The BEST1 promoter limited expression to the RPE. The RPE, photoreceptors, and vascular architecture in both retinal and choroidal compartments were protected. Conditioned medium from RPE-choroid explants, infected by AAV8/BEST1-NRF2, was sufficient to transfer partial protection in vivo, indicating that NRF2 induces a protective secreted factor(s). Analysis of RNA-seq data identified growth differentiation factor 15 (GDF15) as a candidate downstream mediator. Injection of recombinant GDF15 reproduced key protective phenotypes in vivo, whereas Gdf15-deficiency attenuated NRF2-mediated rescue. Pharmacologic inhibition of TGF-{beta} receptor signaling diminished NRF2 associated protection, supporting involvement of this signaling pathway. In a laser-induced choroidal neovascularization model, intravitreal GDF15 injection reduced fluorescein leakage and lesion size. These findings support a model in which NRF2 activation in the RPE induces expression of GDF15, which is capable of protecting the RPE, photoreceptors, and the retinal and choroidal vasculature. NRF2 and GDF15 have therapeutic potential for ocular diseases, as well as for other diseases with vascular pathology.

cell biology↗

bioRxiv2026

Host Endoplasmic Reticulum Stress and Interferon Responses Contribute to AAV-Induced Ocular Toxicity

Adeno-associated viruses (AAVs) are popular gene therapy vectors, but AAVs can cause toxicity. This is particularly evident following expression of some transgenes, e.g. GFP, in the retinal pigment epithelium (RPE), which leads to loss of RPE cells and photoreceptors. Here, we sought to unravel the toxicity mechanism(s). Several transgenes, self and non-self, were tested for toxicity. Some transgenes were toxic while others were not, with no clear correlation for toxicity with regards to self vs non-self transgenes. RPE RNA-sequencing revealed upregulation of translational processes, cell stress, cytokine release, antiviral responses, and leukocyte infiltration pathways. Toxicity-inducing pathways were explored for causality by injecting toxic AAVs into mice deficient for intrinsic, innate, or adaptive immune pathways. The CHOP KO partially alleviated toxicity for RPE but not photoreceptors, whereas the type I interferon receptor KO partially alleviated toxicity for photoreceptors but not RPE. In situ hybridization of interferon pathway transcripts (IFNB1, IFNAR1) revealed that the RPE and retina can produce and potentially respond to interferon. These data suggest that transgene-induced cell stress responses in the RPE lead to RPE cell death, while interferon signaling contributes to the death of photoreceptors.

genetics↗

bioRxiv2026

The evolution of socially modulated dispersal

Dispersal plays a key role in ecology and evolutionary biology, including as a mechanism that reduces local competition. However, dispersers often suffer a fitness disadvantage relative to nondispersers, which may lead individuals to prefer that others disperse rather than dispersing themselves. Hence, if individuals can force their neighbours to disperse, they may be favoured to do so rather than voluntarily dispersing for the good of others. Besides forcing dispersal, individuals might also improve their neighbours ability to disperse. Here, we investigate the evolutionary drivers and consequences of socially modulated dispersal. We find that: (1) there are three possible stable evolutionary outcomes, involving only voluntary dispersal, only socially modulated dispersal, or coexistence of the two; (2) although social modulation that does not improve dispersal success can only be favoured if it is less costly than dispersal itself, social modulation that facilitates dispersal can be favoured even if it is highly expensive for the facilitator; (3) facilitated dispersal may, counterintuitively, lead to a reduced overall level of dispersal; and (4) social modulation can be either welcome or unwelcome from the perspective of the disperser. These predictions emphasise that the evolution of dispersal depends on individuals abilities to both disperse and modulate.

evolutionary biology↗

bioRxiv2025

AAV NRF2 Gene Therapy Preserves Retinal Structure and Function in Rodent Models of Oxidative Damage

Dry age-related macular degeneration is the most frequent cause of visual impairment in individuals over age 50 in developed countries. It is characterized by subretinal deposits of oxidized proteins and lipids and results in progressive loss of high acuity vision. One major risk factor is smoking, which causes oxidative stress in many tissues, including the eye. We previously showed that an adeno-associated viral vector expressing human NRF2 (AAV8/Best1-Nrf2), a transcription factor that regulates responses to oxidative damage, slowed degeneration in mouse models of another blinding disorder, retinitis pigmentosa, which also includes oxidative stress. Here, our AAV8/Best1-Nrf2 vector was tested in a model of oxidative stress wherein sodium iodate was injected systemically, as this is often used to model dry age-related macular degeneration. Sodium iodate causes acute oxidative damage to supporting cells of the retina, the retinal pigment epithelial cells, and ultimately leads to photoreceptor death. Subretinal injection of AAV8/Best1-Nrf2 led to protection of the retinal pigment epithelium and photoreceptors, as well as preservation of visual function, in rat and mouse sodium iodate models. AAV8/Best1-Nrf2 may serve as an effective gene-agnostic therapy for diseases with oxidative stress, including dry age-related macular degeneration. ETOCOxidative stress occurs in diseases that lead to vision loss, including age-related macular degeneration (AMD). AMD is commonly modeled by injection of sodium iodate (S.I.), an oxidizing agent. AAV-mediated delivery of Nrf2, a transcription factor that regulates oxidative stress, protects the eye from S.I. damage in rat and mouse models. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/663952v1_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@357e57org.highwire.dtl.DTLVardef@1f9986dorg.highwire.dtl.DTLVardef@186537corg.highwire.dtl.DTLVardef@1d31aad_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2025

A Congenic C57BL/6 rd1 Mouse Model for Retinal Degeneration Research

Retinitis pigmentosa is an inherited retinal disease caused by thousands of mutations in approximately 100 different genes. The most widely used mouse model for retinitis pigmentosa has the retinal degeneration 1 (rd1) mutation in the Pde6b gene, which elicits rapid retinal degeneration and vision loss. A major limitation of these models is that these rd1 strains are not congenic, which prevents the use of appropriate controls. Furthermore, many strains have mutations in other genes which introduces genetic variability and may confound results. To address this issue, we backcrossed the rd1 allele from FVB mice onto a C57BL/6J genetic background over many generations, producing a C57BL/6J.Pde6brd1 strain that was confirmed to be congenic to C57BL/6J mice. We show that this strain recapitulates the electroretinogram and optomotor results expected for mouse strains containing the rd1 mutation. Examination of retinal structure in cross sections of eyes isolated from C57BL/6J.Pde6brd1 mice show a degree of thinning of the outer nuclear layer expected for a rd1 mutation, resulting in nearly complete loss of the outer nuclear layer by postnatal day 35. We anticipate that this C57BL/6J.Pde6brd1 strain could become an asset for the field of retinitis pigmentosa research.

genetics↗

bioRxiv2024

Mechanistic pathways of tick exposure risk in native and invaded plant communities

Plant invasions may alter disease vector abundance by several mechanistic pathways, including modifying microclimates that influence vector survival or changing habitats to influence host use. Here, we used a field experiment and observational data to evaluate multiple mechanistic pathways (tick survival and host abundance) by which plant invasions may alter vector-borne disease risk using the common disease vector lone star tick (Amblyomma americanum), its preeminent host white-tailed deer (Odocoileus virginianus), and the widespread invasive cogongrass (Imperata cylindrica) in the southeastern USA. In the field experiment, ticks survived over 50% longer in areas dominated by the invasive plant compared to those with only native plant species. Invaded areas had lower temperatures and higher relative humidity, yielding a lower vapor pressure deficit (VPD) that likely reduced tick desiccation. The observational study showed similar average tick abundance in native and invaded plant communities and no difference in wildlife host (white-tailed deer) activity between plant communities. However, there was a positive relationship between tick abundance and white-tailed deer activity, but only in native areas. Together, these results suggest that more favorable microclimate conditions resulting in greater tick longevity are the dominant driver of tick abundance in invaded areas, while tick abundance in native-dominated areas may be promoted, at least in part, by white-tailed deer activity. Our results demonstrate that plant invasions can affect multiple, potentially counteracting mechanistic pathways that contribute to tick exposure risk. The complexity of these relationships highlights the need for better understanding of how invasive species and other global change drivers influence disease vectors and, ultimately, disease transmission.

ecology↗

bioRxiv2024

Paternal genome elimination, monogenic reproduction, and the evolutionary genetics of atypical sex chromosome systems

Sex chromosomes differ from autosomes in both their ploidy and transmission genetics. Consequently, selection, mutation, and drift may act differently upon them, driving distinct patterns in genetic divergence, diversity, and gene content. Recently, researchers have begun to consider a wider set of organisms with non-standard inheritance and sex-determination systems, however in many cases we lack theory which extends to such cases. One such example is paternal genome elimination (PGE), an unusual reproductive system which has independently evolved in two fly families, the fungus gnats (Sciaridae) and gall midges (Cecidomyiidae), and one order of springtails (Symphypleona). Under PGE, males receive but do not transmit a paternal genome, such that the autosomes and X chromosomes exhibit the same transmission genetics, but with different somatic ploidy. This makes them uniquely suited to test hypotheses about the role of haploid selection in males. Additionally, repeatedly throughout these groups a novel sex determination system - monogeny - has evolved, whereby females produce broods of exclusively one sex. The genetic basis of monogeny partitions the X chromosome into three segments, all displaying distinct inheritance patterns. Here we develop a series of theoretical models adapted to the genetics of these groups, generating testable predictions as to the relative genetic diversity within populations, and divergence between populations. Our results suggest that these species are excellent systems with which to test many fundamental principles in evolutionary genetics.

evolutionary biology↗

bioRxiv2024

RPE-specific MCT2 expression promotes cone survival in models of retinitis pigmentosa

Retinitis pigmentosa (RP) is the most common cause of inherited retinal degeneration worldwide. It is characterized by the sequential death of rod and cone photoreceptors, the cells responsible for night and daylight vision, respectively. Although mutations in RP are mostly rod-specific, there is a secondary degeneration of cones. One possible mechanism behind cone death is metabolic dysregulation. Photoreceptors are highly metabolically active, consuming large quantities of glucose and producing substantial amounts of lactate. The retinal pigment epithelium (RPE) mediates the transport of glucose from the blood to photoreceptors and, in turn, removes lactate, which it can use as its own source of fuel. The model for metabolic dysregulation in RP suggests that, following the death of rods, lactate levels are substantially diminished causing the RPE to withhold glucose, resulting in nutrient deprivation for cones. Here, we present adeno-associated viral vector-mediated delivery of monocarboxylate transporter 2 (MCT2) into RPE cells with the aim of promoting lactate uptake from the blood and encouraging the passage of glucose to cones. We demonstrate prolonged survival and function of cones in rat and mouse RP models, revealing a possible gene agnostic therapy for preserving vision in RP. We also present the use of fluorescence lifetime imaging-based biosensors for lactate and glucose within the eye. Using this technology, we show changes to lactate and glucose levels within MCT2-expressing RPE, suggesting cone survival is impacted by RPE metabolism.

neuroscience↗

bioRxiv2024

Kin-discriminating partner choice promotes the evolution of helping

Kin selection theory predicts that individuals should evolve to help relatives, either by helping indiscriminately in a population where they do not move very far from their relatives, or by discriminating kin and conditionally helping them. It has been argued that, because kin discrimination enables individuals to reduce how helpful they are with some social partners as well increase how helpful they are with others, this could lead to an increase or a decrease in the overall level of helping, depending on the curvature of the function relating the optimal level of help and genetic relatedness. However, this prediction was based on a model in which individuals were not able to choose their social partners but only adjust how helpful they should be towards those social partners they have been allocated. Here, we perform a mathematical analysis showing that if kin discriminators are allowed to choose whom they help, kin discrimination is more likely to increase the overall level of helping than previously anticipated. We obtained these results in two complementary theoretical settings: one more general and the other more specific and concrete.

evolutionary biology↗

bioRxiv2023

Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases

Replicative DNA polymerases duplicate entire genomes at high fidelity. This feature is shared among the three domains of life and is facilitated by their dual polymerase and exonuclease activities. Family D replicative DNA polymerases (PolD), found exclusively in Archaea, contain an unusual RNA polymerase-like catalytic core, and a unique Mre11-like proofreading active site. Here, we present cryo-EM structures of PolD trapped in a proofreading mode, revealing an unanticipated correction mechanism that extends the repertoire of protein domains known to be involved in DNA proofreading. Based on our experimental structures, mutants of PolD were designed and their contribution to mismatch bypass and exonuclease kinetics was determined. This study sheds light on the convergent evolution of structurally distinct families of DNA polymerases, and the domain acquisition and exchange mechanism that occurred during the evolution of the replisome in the three domains of life.

molecular biology↗

bioRxiv2023

Kin selection as a modulator of human handedness: sex-specific, parental and parent-of-origin effects

The frequency of left-handedness in humans is [~]10% worldwide and slightly higher in males than females. Twin and family studies estimate the heritability of human handedness at around 25%. The low but substantial frequency of left-handedness has been suggested to imply negative frequency-dependent selection, e.g. owing to a "surprise" advantage of left-handers in combat against opponents more used to fighting right-handers. Because such game-theoretic hypotheses involve social interaction, here, we perform an analysis of the evolution of handedness based on kin-selection, which is understood to play a major role in the evolution of social behaviour generally. We show that: (1) relatedness modulates the balance of right-handedness versus left-handedness, according to whether left- handedness is marginally selfish versus marginally altruistic; (2) sex differences in relatedness to social partners may drive sex differences in handedness; (3) differential relatedness of parents and offspring may generate parent-offspring conflict and sexual conflict leading to the evolution of maternal and paternal genetic effects in relation to handedness; and (4) differential relatedness of maternal-origin versus paternal-origin genes may generate intragenomic conflict leading to the evolution of parent-of-origin-specific gene effects--such as "genomic imprinting"--and associated maladaptation.

evolutionary biology↗

bioRxiv2023

Sexual antagonism in sequential hermaphrodites

Females and males may have distinct phenotypic optima, but share essentially the same complement of genes, potentially leading to trade-offs between attaining high fitness through female versus male reproductive success. Such sexual antagonism may be particularly acute in hermaphrodites, whereby both reproductive strategies are housed within a single individual. Whilst previous models have focused on simultaneous hermaphroditism, we lack theory for how sexual antagonism may play out under sequential hermaphroditism, which have the additional complexities of age-structure. Here we develop a formal theory of sexual antagonism in sequential hermaphrodites. First, we develop a general theoretical overview of the problem, then consider different types of sexually antagonistic and life-history trade-offs, under different modes of genetic inheritance (autosomal or cytoplasmic), and different forms of sequential hermaphroditism (protogynous, protoandrous or bi-directional). Finally, we provide a concrete illustration of these general patterns by developing a two-stage two-sex model, which yields conditions for both invasion of sexually antagonistic alleles and maintenance of sexually antagonistic polymorphisms.

evolutionary biology↗

bioRxiv2022

Electrophysiological Activity of Primary Cortical Neuron-Glia Mixed Cultures

BackgroundWe have previously described a tri-culture of neurons, astrocytes, and microglia that accurately mimics the in vivo neuroinflammatory response (both neurotoxic and neuroprotective) to a wide range of neuroinflammatory stimuli. Electrophysiological activity is an essential measure of neuronal function, which is influenced by neuroinflammation. Microelectrode array (MEA) technology is a versatile tool to non-invasively study in vitro neural networks by simultaneously recording electrophysiological activity from multiple sites. In this study, we used extracellular recordings to determine the effect of microglia on neural network formation and stability in primary cortical cultures and monitor the changes in neural activity in response to neuroinflammatory stimuli. MethodsPrimary neonatal rat cortical tri-cultures of neurons, astrocytes, and microglia or co-cultures of neurons and astrocytes were cultured on custom MEAs and the neural activity was monitored for 21 days in vitro to assess culture maturation and network formation. Quantification of synaptic puncta and averaged spike waveforms were used to determine the difference in excitatory to inhibitory neuron ratio (E/I ratio) of the neurons in tri- and co-cultures. The electrophysiological response to lipopolysaccharide (LPS) treatment of both culture types were compared. ResultsThe tri- and co-culture showed minimal difference in electrophysiological markers of neural network formation and stability with the exception of a significant increase in spike frequency in the tri-culture at later timepoints (DIV 17 and 21). Additionally, there was no significant difference in the density of either post-synaptic or excitatory pre-synaptic puncta between the culture types. However, characterization of the average spike waveforms revealed that the tri-culture had an E/I ratio much closer to that found in the rat cortex. Finally, only the tri-culture displayed a significant decrease in both the number of active channels and spike frequency following LPS exposure. ConclusionsThis study demonstrates that the microglia in the tri-culture do not disrupt neural network formation and stability as quantified using extracellular recordings and may be a better representation of the in vivo cortex due to the closer E/I ratio than more traditional isolated neuron and neuron-astrocyte co-cultures. Additionally, the tri-culture is better able to mimic the neuroinflammatory response to LPS, which was quantified via changes in neural electrophysiological activity.

neuroscience↗

bioRxiv2021

DNA Breaks and Gaps Target Retroviral Integration

Integration into a host genome is essential for retrovirus infection and is catalyzed by a nucleoprotein complex (Intasome) containing the viral integrase (IN) and reverse transcribed (RT) copy DNA (cDNA). Previous studies demonstrated DNA site recognition limited intasome integration. Using single molecule Forster resonance energy transfer (smFRET), we show Prototype Foamy Virus (PFV) intasomes pause at DNA strand breaks and gaps. The break/gap discontinuities are similar to base excision repair (BER) lesion-processing intermediates, which affect retrovirus integration in vivo. Pausing targeted site-directed integration at the break/gap without inducing intasome conformational alterations. An 8-oxo-guanine lesion normally processes by BER and a G/T mismatch or a +T nucleotide insertion that induce flexibility or a bend in the DNA backbone did not promote intasome pausing or targeted integration. These results suggest that repair intermediates can modulate dynamic intasome-DNA interactions which target retroviral integration.

biochemistry↗

bioRxiv2021

How development affects evolution

Natural selection acts on developmentally constructed phenotypes, but how does development affect evolution? This question calls for simultaneous consideration of development and evolution. However, there has been a lack of general mathematical frameworks mechanistically integrating the two, which may have inhibited progress on the question. Here we use a new mathematical framework that mechanistically integrates development into evolution to analyse how development affects evolution. We show that, whilst selection pushes genotypic and phenotypic evolution up the fitness landscape, development determines the admissible evolutionary pathway, such that evolutionary outcomes occur at path peaks rather than landscape peaks. Changes in development can generate path peaks, triggering genotypic or phenotypic diversification, even on constant, single-peak landscapes. Phenotypic plasticity, niche construction, extra-genetic inheritance, and developmental bias alter the evolutionary path and hence the outcome. Thus, extra-genetic inheritance can have permanent evolutionary effects by changing the developmental constraints, even if extra-genetically acquired elements are not transmitted to future generations. Selective development, whereby phenotype construction points in the adaptive direction, may induce adaptive or maladaptive evolution depending on the developmental constraints. Moreover, developmental propagation of phenotypic effects over age enables the evolution of negative senescence. Overall, we find that development plays a major evolutionary role.

evolutionary biology↗

bioRxiv2021

A mathematical framework for evo-devo dynamics

Natural selection acts on phenotypes constructed over development, which raises the question of how development affects evolution. Classic evolutionary theory indicates that development affects evolution by modulating the genetic covariation upon which selection acts, thus affecting genetic constraints. However, whether genetic constraints are relative, thus diverting adaptation from the direction of steepest fitness ascent, or absolute, thus blocking adaptation in certain directions, remains uncertain. This limits understanding of long-term evolution of developmentally constructed phenotypes. Here we formulate a general tractable mathematical framework that integrates age progression, explicit development (i.e., the construction of the phenotype across life subject to developmental constraints), and evolutionary dynamics, thus describing the evolutionary developmental (evo-devo) dynamics. The framework yields simple equations that can be arranged in a layered structure that we call the evo-devo process, whereby five core elementary components generate all equations including those mechanistically describing genetic covariation and the evo-devo dynamics. The framework recovers evolutionary dynamic equations in gradient form and describes the evolution of genetic covariation from the evolution of genotype, phenotype, environment, and mutational covariation. This shows that genotypic and phenotypic evolution must be followed simultaneously to yield a dynamically sufficient description of long-term phenotypic evolution in gradient form, such that evolution described as the climbing of a fitness landscape occurs in "geno-phenotype" space. Genetic constraints in geno-phenotype space are necessarily absolute because the phenotype is related to the genotype by development. Thus, the long-term evolutionary dynamics of developed phenotypes is strongly non-standard: (1) evolutionary equilibria are either absent or infinite in number and depend on genetic covariation and hence on development; (2) developmental constraints determine the admissible evolutionary path and hence which evolutionary equilibria are admissible; and (3) evolutionary outcomes occur at admissible evolutionary equilibria, which do not generally occur at fitness landscape peaks in geno-phenotype space, but at peaks in the admissible evolutionary path where "total genotypic selection" vanishes if exogenous plastic response vanishes and mutational variation exists in all directions of genotype space. Hence, selection and development jointly define the evolutionary outcomes if absolute mutational constraints and exogenous plastic response are absent, rather than the outcomes being defined only by selection. Moreover, our framework provides formulas for the sensitivities of a recurrence and an alternative method to dynamic optimization (i.e., dynamic programming or optimal control) to identify evolutionary outcomes in models with developmentally dynamic traits. These results show that development has major evolutionary effects. HighlightsO_LIWe formulate a framework integrating evolutionary and developmental dynamics. C_LIO_LIWe derive equations describing the evolutionary dynamics of traits considering their developmental process. C_LIO_LIThis yields a description of the evo-devo process in terms of closed-form formulas that are simple and insightful, including for genetic covariance matrices. C_LI

evolutionary biology↗

bioRxiv2021

Sexual antagonism in haplodiploids

Females and males may face different selection pressures, such that alleles conferring a benefit in one sex may be deleterious in the other. Such sexual antagonism has received a great deal of theoretical and empirical attention, almost all of which has focused on diploids. However, a sizeable minority of animals display an alternative haplodiploid mode of inheritance, encompassing both arrhenotoky, whereby males develop from unfertilized eggs, and paternal genome elimination (PGE), whereby males receive but do not transmit a paternal genome. Alongside unusual genetics, haplodiploids often exhibit social ecologies that modulate the relative value of females and males. Here we develop a series of evolutionary-genetic models of sexual antagonism for haplodiploids, incorporating details of their molecular biology and social ecology. We find that: 1) PGE promotes female-beneficial alleles more than arrhenotoky, and to an extent determined by the timing of elimination - and degree of silencing of - the paternal genome; 2) sib-mating relatively promotes female-beneficial alleles, as do other forms of inbreeding, including limited male-dispersal, oedipal-mating, and the pseudo-hermaphroditism of Icerya purchasi; 3) resource competition between related females relatively inhibits female-beneficial alleles; and 4) sexual antagonism foments conflicts between parents and offspring, endosymbionts and hosts, and maternal-origin and paternal-origin genes.

evolutionary biology↗

bioRxiv2020

Comparative genomics of Clostridium species associated with vacuum-packed meat spoilage.

Bacterial species belonging to the Clostridium genera have been recognized as causative agents of blown pack spoilage (BPS) in vacuum packed meat products. Whole-genome sequencing of six New Zealand psychrotolerant Clostridium isolates derived from three meat production animal types and their environments was performed to examine their roles in BPS. Comparative genome analyses have provided insight into the genomic diversity and physiology of these bacteria and divides Clostridia into two separate species clusters. BPS-associated Clostridia encode a large and diverse spectrum of degradative carbohydrate-active enzymes (CAZymes). In total, 516 glycoside hydrolases (GHs), 93 carbohydrate esterases (CEs), 21 polysaccharide lyases (PLs), 434 glycosyl transferases (GTs) and 211 carbohydrate-binding protein modules (CBM) with predicted activities involved in the breakdown and transport of carbohydrates were identified. Clostridia genomes have different patterns of CAZyme families and vary greatly in the number of genes within each CAZy category, suggesting some level of functional redundancy. These results suggest that BPS-associated Clostridia occupy similar environmental niches but apply different carbohydrate metabolism strategies to be able to co-exist and cause meat spoilage.

microbiology↗