Gut Microbiome Of Animals Research Articles

Cross‐scale scaling‐law analyses for the heterogeneity and diversity of animal gut microbiomes from community to landscape

Diversity and heterogeneity often are conflated but are fundamentally different. An aphorism proposed by Shavit and Ellison (2021; J. Phil. 118: 525–548) for distinguishing them is that ‘a zoo is diverse whereas an ecosystem is heterogeneous.' That is, a zookeeper measuring diversity simply enumerates the different types of animals; interactions are not expected to occur between animals separated by fences or other barriers. In contrast, measures of heterogeneity ought to include both interspecific interactions and relationships between species and their heterogeneous habitats. Here, we use cross‐scale, dual scaling‐law analyses of heterogeneity and diversity of animal gut microbiomes (AGMs) to address three objectives: 1) estimate the spatial heterogeneity and diversity of animal‐gut microbiomes; 2) analyze influences of phylogeny and diets on scaling of diversity and heterogeneity; 3) explore mechanistic differences between diversity and heterogeneity in AGMs. From 4903 AGM samples collected from 318 animal species covering all six classes of vertebrates and four major classes of invertebrates, we estimated that ≈640 000 operational taxonomic units (OTUs or ‘species') make up the pool of microbial species that could inhabit animal guts, among which ≈8000 are relatively common and ≈800 are dominant. The gut of any single animal, however, includes only 0.01–0.5% of the total species pool. We applied Ma's diversity‐area relationship for scaling diversity, and extend Taylor's power law and Luna et al.'s (2020; Diversity 12: 86) interaction diversity for scaling heterogeneity. At the community scale, phylogeny significantly influenced heterogeneity, but diets did not. Phylogeny and diets had limited influence on diversity at both community and landscape scales. We demonstrated that diversity and heterogeneity measure two different properties. Further, differences in scaling of diversity and heterogeneity are a result of heterogeneity being primarily the result of evolved dispersal behavior and interspecific interactions, whereas diversity results from abundances controlled on ecological time scales.

Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices.

Comparative approaches in animal gut microbiome research have revealed patterns of phylosymbiosis, dietary and physiological convergences, and environment-host interactions. However, most large-scale comparative studies, especially those that are highly cited, have focused on mammals, and efforts to integrate comparative approaches with existing ecological frameworks are lacking. While mammals serve as useful model organisms, developing generalised principles of how animal gut microbiomes are shaped and how these microbiomes interact bidirectionally with host ecology and evolution requires a more complete sampling of the animal kingdom. Here, we provide an overview of what past comparative studies have taught us about the gut microbiome, and how community ecology theory may help resolve certain contradictions in comparative gut microbiome research. We explore whether certain hypotheses are supported across clades, and how the disproportionate focus on mammals has introduced potential bias into gut microbiome theory. We then introduce a methodological solution by which public gut microbiome data of understudied hosts can be compiled and analysed in a comparative context. Our aggregation and analysis of 179 studies shows that generating data sets with rich host diversity is possible with public data and that key gut microbes associated with mammals are widespread across the animal kingdom. We also show the effects that sample size and taxonomic rank have on comparative gut microbiome studies and that results of multivariate analyses can vary significantly with these two parameters. While challenges remain in developing a universal model of the animal gut microbiome, we show that existing ecological frameworks can help bring us one step closer to integrating the gut microbiome into animal ecology and evolution.

Diverse microviruses circulating in invertebrates within a lake ecosystem.

Microviruses are single-stranded DNA bacteriophages and members of the highly diverse viral family Microviridae. Microviruses have a seemingly ubiquitous presence across animal gut microbiomes and other global environmental ecosystems. Most of the studies on microvirus diversity so far have been associated with vertebrate gut viromes. In this study, we investigate the less explored invertebrate microviruses in a freshwater ecosystem. We analysed microviruses from invertebrates in the Chironomidae, Gastropoda, Odonata, Sphaeriidae, Unionidae clades, as well as from water and benthic sediment sampled from a lake ecosystem in New Zealand. Using gene-sharing networks and an expanded framework of informal and proposed microvirus subfamilies, the 463 distinct microvirus genomes identified in this study were grouped as follows: 382 genomes in the Gokushovirinae subfamily and 47 in the Pichovirinae subfamily clade, 18 belonging to Group D, 3 belonging to the proposed Alpavirinae subfamily clade, 1 belonging to the proposed Occultatumvirinae/Tainavirinae subfamilies clade and 12 belonging to an undefined viral cluster VC 1. Inverse associations of microviruses were noted between environmental benthic sediment samples and the Odonata group, while 'defended' invertebrates in the Gastropoda, Sphaeriidae and Unionidae groups showed correlative associations in the principal coordinate analysis of unique microvirus genomes (each genome sharing <98% genome-wide pairwise identity with each other) across sample types. This study expands the known diversity of microviruses and highlights the diversity of these relatively poorly classified bacteriophages.

NpmC, a novel A1408 16S rRNA methyltransferase in the gut of humans and animals

16S rRNA methyltransferases that act on residue A1408, NpmA and NpmB, confer high-level resistance to virtually all the aminoglycosides, but their reports are scarce. Analysing metagenomic projects in a One Health context, we identified in human and animal gut microbiomes from China and Canada a novel gene, npmC, that shares an identity of 91.5% with npmA, and up to 92.7% at amino acidic level. The protein encoded by this gene presents the conserved motifs required for A1408 methylation. Expression of the gene resulted in high-level of resistance to 4,5-disubstituted 2-deoxystreptamine (2-DOS) and to 4-monosubstituted 2-DOS aminoglycosides, as well as a moderate resistance to 4,6-disusbstituted 2-DOS aminoglycosides, including the last resort aminoglycoside plazomicin. Methylation at residue A1408 was further confirmed by mass spectrometry assays. The analysis of the npmC gene background revealed that its genetic context is associated to different insertion sequences that could mobilise it. Similarities in the genetic context between npmC and npmA suggest that they share a common ancestor. The immediate genetic context of this methyltransferase suggests high relationship to the Eubacteriales order. This finding enlarges the list of the true pan-aminoglycoside 16S rRNA methyltransferases, that threaten the usefulness and development of next-generation aminoglycosides.

Altitude shapes gut microbiome composition accounting for diet, thyroid hormone levels, and host genetics in a subterranean blind mole rat.

The animal gut microbiome acts as a crucial link between the host and its environment, playing a vital role in digestion, metabolism, physiology, and fitness. Using 16S rRNA metabarcoding, we investigated the effect of altitude on the microbiome composition of Anatolian Blind Mole Rats (Nannospalax xanthodon) across six locations and three altitudinal groups. We also factored in the host diet, as well as host microsatellite genotypes and thyroid hormone levels. The altitude had a major effect on microbiome composition, with notable differences in the relative abundance of several bacterial taxa across elevations. Contrary to prior research, we found no significant difference in strictly anaerobic bacteria abundance among altitudinal groups, though facultatively anaerobic bacteria were more prevalent at higher altitudes. Microbiome alpha diversity peaked at mid-altitude, comprising elements from both low and high elevations. The beta diversity showed significant association with the altitude. Altitude had a significant effect on the diet composition but not on its alpha diversity. No distinct altitude-related genetic structure was evident among the host populations, and no correlation was revealed between the host genetic relatedness and microbiome composition nor between the host microbiome and the diet. Free thyroxine (FT4) levels increased almost linearly with the altitude but none of the bacterial ASVs were found to be specifically associated with hormone levels. Total thyroxine (TT4) levels correlated positively with microbiome diversity. Although we detected correlation between certain components of the thyroid hormone levels and the microbiome beta diversity, the pattern of their relationship remains inconclusive.

Seasonal variations in composition and function of gut microbiota in grazing yaks: Implications for adaptation to dietary shift on the Qinghai-Tibet plateau.

Gut microbiome of animals is affected by external environmental factors and can assist them in adapting to changing environments effectively. Consequently, elucidating the gut microbes of animals under different environmental conditions can provide a comprehensive understanding of the mechanisms of their adaptations to environmental change, with a particular focus on animals in extreme environments. In this study, we compared the structural and functional differences of the gut microbiome of grazing yaks between the summer and winter seasons through metagenomic sequencing and bioinformatics analysis. The results indicated that the composition and function of microbes changed significantly. The study demonstrated an increase in the relative abundance of Actinobacteria and a higher ratio of Firmicutes to Bacteroidetes (F/B) in winter, this process facilitated the adaptation of yaks to the consumption of low-nutrient forages in the winter. Furthermore, the network structure exhibited greater complexity in the winter. Forage nutrition exhibited a significant seasonal variation, with a notable impact on the gut microbiota. The metagenomic analysis revealed an increase in the abundance of enzymes related to amino acid metabolism, axillary activity, and mucin degradation in the winter. In conclusion, this study demonstrated that the gut microbiome of grazing yaks exhibits several adaptive characteristics that facilitate better nutrient accessibility and acid the host in acclimating to the harsh winter conditions. Furthermore, our study offers novel insights into the mechanisms of highland animal adaptation to external environments from the perspective of the gut microbiome.

The Role of Geography, Diet, and Host Phylogeny on the Gut Microbiome in the Hawaiian Honeycreeper Radiation.

The animal gut microbiome can have a strong influence on the health, fitness, and behavior of its hosts. The composition of the gut microbial community can be influenced by factors such as diet, environment, and evolutionary history (phylosymbiosis). However, the relative influence of these factors is unknown in most bird species. Furthermore, phylosymbiosis studies have largely focused on clades that diverged tens of millions of years ago, and little is known about the degree of gut microbiome divergence in more recent species radiations. This study explores the drivers of microbiome variation across the unique and recent Hawaiian honeycreeper radiation (Fringillidae: Drepanidinae). Fecal samples were collected from 14 extant species spanning the main islands of the Hawaiian archipelago and were sequenced using three metabarcoding markers to characterize the gut microbiome, invertebrate diet, and plant diet of Hawaiian honeycreepers. We then used these metabarcoding data and the honeycreeper host phylogeny to evaluate their relative roles in shaping the gut microbiome. Microbiome variation across birds was highly individualized; however, source island had a small but significant effect on microbiome structure. The microbiomes did not recapitulate the host phylogenetic tree, indicating that evolutionary history does not strongly influence microbiome structure in the honeycreeper clade. These results expand our understanding of the roles of diet, geography, and phylogeny on avian microbiome structure, while also providing important ecological information about the diet and gut microbiota of wild Hawaiian honeycreepers.

Host diet drives gut microbiome convergence between coral reef fishes and mammals.

Animal gut microbiomes are critical to host physiology and fitness. The gut microbiomes of fishes-the most abundant and diverse vertebrate clade-have received little attention relative to other clades. Coral reef fishes, in particular, make up a wide range of evolutionary histories and feeding ecologies that are likely associated with gut microbiome diversity. The repeated evolution of herbivory in fishes and mammals also allows us to examine microbiome similarity in relationship to diet across the entire vertebrate tree of life. Here, we generate a large coral reef fish gut microbiome dataset (n = 499 samples, 19 species) and combine it with a diverse aggregation of public microbiome data (n = 447) to show that host diet drives significant convergence between coral reef fish and mammalian gut microbiomes. We demonstrate that this similarity is largely driven by carnivory and herbivory and that herbivorous and carnivorous hosts exhibit distinct microbial compositions across fish and mammals. We also show that fish and mammal gut microbiomes share prominent microbial taxa, including Ruminoccocus spp. and Akkermansia spp., and predicted metabolic pathways. Despite the major evolutionary and ecological differences between fishes and mammals, our results reveal that their gut microbiomes undergo similar dietary selective pressures. Thus, diet, in addition to phylosymbiosis must be considered even when comparing the gut microbiomes of distantly related hosts.

A decade of advances in black soldier fly research: from genetics to sustainability

Abstract Black soldier fly (BSF), Hermetia illucens, is one of the most explored insect species mass-produced for feed, but also for food and technical purposes. Considering the rapid developments in both research and industrial production of this insect species in the last decade, this review intends to reflect on the most current scientific insights and define the future trends and needs for the most relevant associated research fields. The review reflects on the aspects of BSF production and reproduction, utilization of BSF biomass as components of animals’ feeds and human food. It also provides reflection on genetics, microbiology and sustainability. The analysis identifies the need in future research associated with compositions of fungal and viral communities of insects and their environments and mapping the dynamics of BSF gut physiology and microbiota in varying conditions. High interest will be devoted to establishing genomic resources, to characterize genotypic diversity, and to harness its potential through selective breeding to improve BSF performance quantitatively and/or qualitatively. Further research will follow on the use of BSF for food and feed development, potentially for specific application cases, associated with animal gut microbiome improvement and antimicrobial properties of BSF biomass. The further in-depth exploration of the potential of BSF for waste biotransformation and the assessment of its circularity potential are also expected to be major focus points of research in the next decade.

Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system.

Providencia alcalifaciens is a Gram-negative bacterium found in a wide variety of water and land environments and organisms. It has been isolated as part of the gut microbiome of animals and insects, as well as from stool samples of patients with diarrhea. Specific P. alcalifaciens strains encode gene homologs of virulence factors found in other pathogenic members of the same Enterobacterales order, such as Salmonella enterica serovar Typhimurium and Shigella flexneri. Whether these genes are also pathogenic determinants in P. alcalifaciens is not known. Here we have used P. alcalifaciens 205/92, a clinical isolate, with in vitro and in vivo infection models to investigate P. alcalifaciens -host interactions at the cellular level. Our particular focus was the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS 1b is widespread in Providencia spp. and encoded on the chromosome. T3SS 1a is encoded on a large plasmid that is present in a subset of P. alcalifaciens strains, which are primarily isolates from diarrheal patients. Using a combination of electron and fluorescence microscopy and gentamicin protection assays we show that P. alcalifaciens 205/92 is internalized into eukaryotic cells, rapidly lyses its internalization vacuole and proliferates in the cytosol. This triggers caspase-4 dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS 1a in entry, vacuole lysis and cytosolic proliferation is host-cell type specific, playing a more prominent role in human intestinal epithelial cells as compared to macrophages. In a bovine ligated intestinal loop model, P. alcalifaciens colonizes the intestinal mucosa, inducing mild epithelial damage with negligible fluid accumulation. No overt role for T3SS 1a or T3SS 1b was seen in the calf infection model. However, T3SS 1b was required for the rapid killing of Drosophila melanogaster . We propose that the acquisition of two T3SS by horizontal gene transfer has allowed P. alcalifaciens to diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.

The underlying causes, treatment options of gut microbiota and food habits in type 2 diabetes mellitus: a narrative review.

Type 2 diabetes mellitus is a long-lasting endocrine disorder characterized by persistent hyperglycaemia, which is often triggered by an entire or relative inadequacy of insulin production or insulin resistance. As a result of resistance to insulin (IR) and an overall lack of insulin in the body, type 2 diabetes mellitus (T2DM) is a metabolic illness that is characterized by hyperglycaemia. Notably, the occurrence of vascular complications of diabetes and the advancement of IR in T2DM are accompanied by dysbiosis of the gut microbiota. Due to the difficulties in managing thedisease and the dangers of multiple accompanying complications, diabetes is a chronic, progressive immune-mediated condition that plays a significant clinical and health burden on patients. The frequency and incidence of diabetes among young people have been rising worldwide. The relationship between the gut microbiota composition and the physio-pathological characteristics of T2DM proposes a novel way to monitor the condition and enhance the effectiveness of therapies. Our knowledge of the microbiota of the gut and how it affects health and illness has changed over the last 20 years. Species of the genus Eubacterium, which make up a significant portion of the core animal gut microbiome, are some of the recently discovered 'generation' of possibly helpful bacteria. In this article, we have focused on pathogenesis and therapeutic approaches towards T2DM, with a special reference to gut bacteria from ancient times to the present day.

The Profound Influence of Gut Microbiome and Extracellular Vesicles on Animal Health and Disease.

The animal gut microbiota, comprising a diverse array of microorganisms, plays a pivotal role in shaping host health and physiology. This review explores the intricate dynamics of the gut microbiome in animals, focusing on its composition, function, and impact on host-microbe interactions. The composition of the intestinal microbiota in animals is influenced by the host ecology, including factors such as temperature, pH, oxygen levels, and nutrient availability, as well as genetic makeup, diet, habitat, stressors, and husbandry practices. Dysbiosis can lead to various gastrointestinal and immune-related issues in animals, impacting overall health and productivity. Extracellular vesicles (EVs), particularly exosomes derived from gut microbiota, play a crucial role in intercellular communication, influencing host health by transporting bioactive molecules across barriers like the intestinal and brain barriers. Dysregulation of the gut-brain axis has implications for various disorders in animals, highlighting the potential role of microbiota-derived EVs in disease progression. Therapeutic approaches to modulate gut microbiota, such as probiotics, prebiotics, microbial transplants, and phage therapy, offer promising strategies for enhancing animal health and performance. Studies investigating the effects of phage therapy on gut microbiota composition have shown promising results, with potential implications for improving animal health and food safety in poultry production systems. Understanding the complex interactions between host ecology, gut microbiota, and EVs provides valuable insights into the mechanisms underlying host-microbe interactions and their impact on animal health and productivity. Further research in this field is essential for developing effective therapeutic interventions and management strategies to promote gut health and overall well-being in animals.

Transmission rates of veterinary and clinically important antibiotic resistant Escherichia coli: A meta- ANALYSIS

The transmission rate per hour between hosts is a key parameter for simulating transmission dynamics of antibiotic-resistant bacteria, and might differ for antibiotic resistance genes, animal species, and antibiotic usage. We conducted a Bayesian meta-analysis of resistant Escherichia coli (E. coli) transmission in broilers and piglets to obtain insight in factors determining the transmission rate, infectious period, and reproduction ratio. We included blaCTX-M-1, blaCTX-M-2, blaOXA-162, catA1, mcr-1, and fluoroquinolone resistant E. coli. The Maximum a Posteriori (MAP) transmission rate in broilers without antibiotic treatment ranged from 0.4∙10−3 to 2.5∙10−3 depending on type of broiler (SPF vs conventional) and inoculation strains. For piglets, the MAP in groups without antibiotic treatment were between 0.7∙10−3 and 0.8∙10−3, increasing to 0.9∙10−3 in the group with antibiotic treatment. In groups without antibiotic treatment, the transmission rate of resistant E. coli in broilers was almost twice the transmission rate in piglets. Amoxicillin increased the transmission rate of E. coli carrying blaCTX-M-2 by three-fold. The MAP infectious period of resistant E. coli in piglets with and without antibiotics is between 971 and 1065 hours (40 – 43 days). The MAP infectious period of resistant E. coli in broiler without antibiotics is between 475 and 2306 hours (20 – 96 days). The MAP infectious period of resistant E. coli in broiler with antibiotics is between 2702 and 3462 hours (113 – 144 days) which means a lifelong colonization. The MAP basic reproduction ratio in piglets of infection with resistant E. coli when using antibiotics is 27.70, which is higher than MAP in piglets without antibiotics between 15.65 and 18.19. The MAP basic reproduction ratio in broilers ranges between 3.46 and 92.38. We consider three possible explanations for our finding that in the absence of antibiotics the transmission rate is higher among broilers than among piglets: i) due to the gut microbiome of animals, ii) fitness costs of bacteria, and iii) differences in experimental set-up between the studies. Regarding infectious period and reproduction ratio, the effect of the resistance gene, antibiotic treatment, and animal species are inconclusive due to limited data.

Clinical use of tigecycline may contribute to the widespread dissemination of carbapenem-resistant hypervirulent Klebsiella pneumoniae strains

ABSTRACT The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) poses grave threats to human health. These strains increased dramatically in clinical settings in China in the past few years but not in other parts of the world. Four isogenic K. pneumoniae strains, including classical K. pneumoniae, carbapenem-resistant K. pneumoniae (CRKP), hypervirulent K. pneumoniae (hvKP) and CR-hvKP, were created and subjected to phenotypic characterization, competition assays, mouse sepsis model and rat colonization tests to investigate the mechanisms underlying the widespread nature of CR-hvKP in China. Acquisition of virulence plasmid led to reduced fitness and abolishment of colonization in the gastrointestinal tract, which may explain why hvKP is not clinically prevalent after its emergence for a long time. However, tigecycline treatment facilitated the colonization of hvKP and CR-hvKP and reduced the population of Lactobacillus spp. in animal gut microbiome. Feeding with Lactobacillus spp. could significantly reduce the colonization of hvKP and CR-hvKP in the animal gastrointestinal tract. Our data implied that the clinical use of tigecycline to treat carbapenem-resistant K. pneumoniae infections facilitated the high spread of CR-hvKP in clinical settings in China and demonstrated that Lactobacillus spp. was a potential candidate for anticolonization strategy against CR-hvKP.

Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods.

The gut microbiome of companion animals is relatively underexplored, despite its relevance to animal health, pet owner health, and basic microbial community biology. Here, we provide the most comprehensive analysis of the canine and feline gut microbiomes to date, incorporating 2639 stool shotgun metagenomes (2272 dog and 367 cat) spanning 14 publicly available datasets (n = 730) and 8 new study populations (n = 1909). These are compared with 238 and 112 baseline human gut metagenomes from the Human Microbiome Project 1-II and a traditionally living Malagasy cohort, respectively, processed in a manner identical to the animal metagenomes. All microbiomes were characterized using reference-based taxonomic and functional profiling, as well as de novo assembly yielding metagenomic assembled genomes clustered into species-level genome bins. Companion animals shared 184 species-level genome bins not found in humans, whereas 198 were found in all three hosts. We applied novel methodology to distinguish strains of these shared organisms either transferred or unique to host species, with phylogenetic patterns suggesting host-specific adaptation of microbial lineages. This corresponded with functional divergence of these lineages by host (e.g. differences in metabolic and antibiotic resistance genes) likely important to companion animal health. This study provides the largest resource to date of companion animal gut metagenomes and greatly contributes to our understanding of the "One Health" concept of a shared microbial environment among humans and companion animals, affecting infectious diseases, immune response, and specific genetic elements.

Diversity of gut microbiome in Rocky Mountainsnail across its native range.

The animal gut microbiome is often a key requirement for host nutrition, digestion, and immunity, and can shift in relation to host geography and environmental factors. However, ecological drivers of microbiome community assembly across large geographic ranges have rarely been examined in invertebrates. Oreohelix strigosa (Rocky Mountainsnail) is a widespread land snail found in heterogeneous environments across the mountainous western United States. It is ideally suited for biogeography studies due to its broad distribution, low migration, and low likelihood of passive transport via other animals. This study aims to uncover large-scale geographic shifts in the composition of O. strigosa gut microbiomes by using 16S rRNA gene sequencing on samples from across its native range. Additionally, we elucidate smaller-scale microbiome variation using samples collected only within Colorado. Results show that gut microbiomes vary significantly across broad geographic ranges. Several possible ecological drivers, including soil and vegetation composition, habitat complexity, habitat type, and human impact, collectively explained 27% of the variation across Coloradan O. strigosa gut microbiomes. Snail gut microbiomes show more similarity to vegetation than soil microbiomes. Gut microbial richness was highest in the rocky habitats and increased significantly in the most disturbed habitats (low complexity, high human impact), potentially indicating signs of dysbiosis in the snails' gut microbiomes. These small-scale environmental factors may be driving changes in O. strigosa gut microbiome composition seen across large-scale geography. This knowledge will also help us better understand how microbial associations influence species survival in diverse environments and aid wildlife conservation efforts.

19 The Swine Gut Microbiome and Animal Production

Abstract Recent studies have dramatically improved our understanding of the swine gut microbiome regarding its composition and correlations with animal phenotypes. However, many basic biological and ecological questions still remain to be answered. In addition, it is even challenging to translate basic gut microbiome research into industrial applications. During my presentation, I will first address several important ecological questions in two animal trials: a longitudinal study and a fecal microbiota transplantation experiment. Through big data analysis, we identified a probiotic candidate that correlates well with growth performance. We then re-analyzed two published data sets from other animal trials (isolated rearing and ZnO treatment). All four animal trials show a positive correlation between an F2 strain with growth performance. We isolated 200 F2 strains using a culturomics approach developed in my lab to establish a causal relationship between F2 and the host. After in vitro characterization of these isolates and whole genome sequencing, we conducted three animal trials to validate their probiotic effects and explore their underlying mechanisms. At the end of my presentation, I will discuss the future directions of animal gut microbiome.

RNAseq analysis of Cellvibrio japonicus during starch utilization differentiates between genes encoding carbohydrate active enzymes controlled by substrate detection or growth rate.

Understanding the bacterial metabolism of starch is important as this polysaccharide is a ubiquitous ingredient in foods, supplements, and medicines, all of which influence gut microbiome composition and health. Our RNAseq and growth data set provides a valuable resource to those who want to better understand the regulation of starch utilization in Gram-negative bacteria. These data are also useful as they provide an example of how to approach studying a starch-utilizing bacterium that has many putative amylases by coupling transcriptomic data with growth assays to overcome the potential challenges of functional redundancy. The RNAseq data can also be used as a part of larger meta-analyses to compare how C. japonicus regulates carbohydrate active enzymes, or how this bacterium compares to gut microbiome constituents in terms of starch utilization potential.

Network complexity of bacterial community driving antibiotic resistome in the microbiome of earthworm guts under different land use patterns

Recently, the study of antibiotic resistance in the soil animal microbiome has attracted extensive attention; however, the patterns of antibiotic resistance genes (ARGs) in soil and soil animals related to different land use types remain poorly studied. In the present study, soil and earthworms were collected from four different land-use types (farmland, hospital, park land, and mountain park), and 162 ARGs in the microbiomes of the soil and earthworms were quantified using high-throughput quantitative PCR. Our study showed that the abundance and number of ARGs were higher in soil samples than in earthworm guts, but earthworms as the living organisms created relatively isolated ambient surroundings, which allowed for a more heterogeneous ARGs profile. Meanwhile, land use significantly influenced the abundance, number and co-occurrence pattern of ARGs in the soil and earthworm samples. Furthermore, abiotic and biotic factors had significant effects on the ARGs profile, among which pH had a negative effect on the ARGs profiles of both soil and earthworm microbiomes, and bacterial network complexity had a positive effect on the earthworm ARGs profile. Our study provides new insights into the distribution and dispersal of ARGs in the soil animal gut microbiome under different land use patterns.

Guidelines for Microbiome Studies in Renal Physiology.

Gut microbiome research has increased dramatically in the last decade, including in renal health and disease. The field is moving from experiments showing mere association to causation using both forward and reverse microbiome approaches, leveraging tools such as germ-free animals, treatment with antibiotics, and faecal microbiota transplantations. However, we are still seeing a gap between discovery and translation that needs to be addressed, so that patients can benefit from microbiome-based therapies. In this guideline paper, we discuss the key considerations that affect the gut microbiome of animal and clinical studies assessing renal function, many which are often overlooked, resulting in false-positive results. For animal studies, these include suppliers, acclimatisation, baseline microbiota and its normalisation, littermates and cohort/cage effects, diet, sex differences, age, circadian differences, antibiotics and sweeteners, and models used. Clinical studies have some unique considerations, which include sampling, gut transit time, dietary records, medication, and renal phenotypes. We provide best practice guidance on sampling, storage, DNA extraction, and methods for microbial DNA sequencing (both 16S rRNA and shotgun metagenome). Finally, we discuss follow-up analyses, including tools available, metrics, and their interpretation, and the key challenges ahead in the microbiome field. By standardising study designs, methods and reporting, we will accelerate the findings from discovery to translation and result in new microbiome-based therapies that may improve renal health.