In-feed antibiotic effects on the swine intestinal microbiome

Distribution of antibiotic resistance genes on chromosomes, plasmids and phages in aerobic biofilm microbiota under antibiotic pressure

The objective of this study is to quantitatively reveal the main genetic carrier of antibiotic resistance genes (ARGs) for blocking their environmental dissemination. The distribution of ARGs in chromosomes, plasmids, and phages for understanding their respective contributions to the development of antimicrobial resistance in aerobic biofilm consortium under increasing stresses of oxytetracycline, streptomycin, and tigecycline were revealed based on metagenomics analysis. Results showed that the plasmids harbored 49.2 %-83.9 % of resistomes, which was higher (p < 0.001) than chromosomes (2.0 %-35.6 %), and no ARGs were detected in phage contigs under the strict alignment standard of over 80 % identity used in this study. Plasmids and chromosomes tended to encode different types of ARGs, whose abundances all increased with the hike of antibiotic concentrations, and the variety of ARGs encoded by plasmids (14 types and 64 subtypes) was higher than that (11 types and 27 subtypes) of chromosomes. The dosing of the three antibiotics facilitated the transposition and recombination of ARGs on plasmids, mediated by transposable and integrable transfer elements, which increased the co-occurrence of associated and unassociated ARGs. The results quantitatively proved that plasmids dominate the proliferation of ARGs in aerobic biofilm driven by antibiotic selection, which should be a key target for blocking ARG dissemination.

Towards a unified approach in managing resistance to vaccines, drugs, and pesticides

Everywhere, pests and pathogens evolve resistance to our control efforts, impairing human health and welfare. Developing sustainable solutions to this problem requires working with evolved immune and ecological systems, rather than against these evolutionary forces. We advocate a transdisciplinary approach to resistance based on an evolutionary foundation informed by the concepts of integrated pest management and One Health. Diverse, multimodal management approaches create a more challenging environment for the evolution of resistance. Given our permanent evolutionary and ecological relationships with pests and pathogens, responses to most biological threats to health and agriculture should seek sustainable harm reduction rather than eradication.

Biodegradation characterization and mechanism of low-density polyethylene by the enriched mixed-culture from plastic-contaminated soil

Plastic pollution poses significant ecological and health risks. In this study, we enriched microbial consortia from plastic-contaminated soil capable of degrading low-density polyethylene (LDPE) film over a 28-day incubation period. Using two kinds of enriched cultures, the mean film weight loss rate (WLR) of 0.27 ± 0.04 % (p < 0.01) was 9 times higher than the control. Scanning electron microscopy (SEM) revealed a average hole occurrence area of 0.67 ± 0.11 μm2 in the topmost sample, while the control had no change. Fourier transform infrared (FTIR) revealed specific changes in hydrophilicity (increased by 5.70 ± 0.02 times) and crystallinity (decreased by 15.73 ± 3.26 %). Meanwhile, FTIR analyses including peak occurrence at 3741 cm-1, carbonyl index and Lambert-Beer law calculations revealed moisture infiltration and predominant aldehyde carbonyl formation (88.69 % in total carbonyl). The results of high-throughput sequencing indicated Brevibacillus, Bacillus and Sporosarcina were dominate genera in the mixed-cultures, and PICRUSt2 implied they could use LDPE as the sole carbon source. Our study aims to provided theoretical basis driving plastic degradation and to mitigate plastic pollution based on microbial resource development.

Manure application primarily drives changes in antibiotic resistome composition rather than abundance in agricultural soil profile

The prevalence of antibiotic resistance genes (ARGs) in soil has elicited significant concerns about food safety and agricultural sustainability. However, the impact of long-term fertilization on the soil resistome across soil profiles and their associations with both abundant and rare microbial taxa remain unknown. This study employed high-throughput quantitative polymerase chain reaction (HT-qPCR) and 16S rRNA gene sequencing to explore resistome across soil depths under different fertilization regimes (a 12-year field experiment). Compared with the control and chemical-only fertilization, manure amendment increased the ARG richness in the topsoil by 14.1-20 % but had no significant effect on the subsoil. Manure amendment resulted eight unique ARGs into topsoil: sul1, sul2, aadA, aadA2, aadA21, APHA3, ErmY and qacF_H. Compared with the control soil, the manure amendment did not increase the absolute and normalized abundance of ARGs in both top- and subsoil. In addition, abundant microbial taxa exhibited a stronger association with ARGs than rare taxa. Overall, manure amendment had strong and direct impacts on soil ARG composition and indirectly influenced ARG abundance to a limited extent through its effects on soil properties and abundant taxa. These findings strengthen our understanding of the ecological impacts of long-term fertilization and inform sustainable agricultural practices.

Insights into the impact of different phytoremediation strategies on antibiotic resistance genes at the metagenomic level in real scenarios

Engineered phytoremediation strategies provide cost effective options for eliminating antibiotics and antibiotic resistance genes (ARGs) from wastewater. However, there is a knowledge gap in understanding the impact of these phytoremediation strategies on the on the diversity and composition of ARGs as well as the key driving biotic and biological factors of ARGs at the metagenomic level in real scenarios. Through metagenomic sequencing, this study demonstrates that phytoremediation with Iris pseudacorus L., Myriophyllum verticillatum L., Eichhornia crassipes (Mart.) Solms and Oenanthe javanica (Bl. DC) significantly alters the pattern of antibiotic resistome. This study is the first to reveal, at the omics level, that phytoremediation enhances the diversity of ARGs (3.2 %∼11.6 % improvement), despite reducing their absolute abundances. Furthermore, this study highlights that plant varieties have a significant impact on the performance of phytoremediation in mitigating ARGs. The non-dominant bacterial taxa, specifically Verrucomicrobia, Planctomycetes, and Actinobacteria, play a crucial role in shaping the pattern of the antibiotic resistome during the wastewater treatment. The changes in the total organic carbon, total nitrogen and antibiotics robustly influence the environmental behaviors of antibiotic resistome and microbiome. In summary, this study gives insight into the impact of different phytoremediation strategies on mitigating ARGs at the omics level in real scenarios.

Antimicrobial Resistance in Diverse Ecological Niches-One Health Perspective and Food Safety

Antimicrobial resistance (AMR) is a multi-sectoral, systemic, and global issue worldwide. Antimicrobial use (AMU) is a key factor in the selection of resistant bacteria within different ecological niches, from agriculture to food-producing animals to humans. There is a question regarding the extent to which the use of antibiotics in livestock production and the primary food production sector influences the selection and transmission of resistant bacteria and/or resistant genes throughout the food chain and thus contributes to the complexity in the development of AMR in humans. Although the trends in the prevalence of foodborne pathogens have changed over time, the burden of ecological niches with resistance genes, primarily in commensal microorganisms, is of concern. The implementation of the harmonized surveillance of AMU and AMR would provide comprehensive insights into the actual status of resistance and further interventions leading to its reduction. Tracking AMR in different ecological niches by applying advanced genome-based techniques and developing shared AMR data repositories would strengthen the One Health concept.

Probiotic Lactocaseibacillus casei NK1 Enhances Growth and Gut Microbiota in Avian Pathogenic Escherichia coli Challenged Broilers

The present study was conducted to assess the efficacy of Laboratory-Isolated Lactocaseibacillus casei NK1 (Lc. NK1) in broilers hypothesizing that, Lc. NK1 supplementation will enhance growth performance, modulate the gut microbiome, and reduce fecal pathogenic Escherichia coli in broilers. The experiment spanned 35 days where 60 one-day-old broiler chicks were randomly assigned to four treatment groups (n = 15); control-group with no treatment (NC), APEC (challenged with E. coli only), CProb (received commercial probiotics), and LNK1 (treated with Lc. NK1). The APEC, CProb, and LNK1 groups were infected with E. coli O78 strain at 11 days of age. Growth performance analysis revealed that the LNK1 group by day 35 gained body weight similar to the CProb group, with both groups significantly outperforming the APEC group (p < 0.001). Both the LNK1 and CProp groups exhibited similar reduction in E. coli while increasing Lactobacillus colorizations in the cloacal swabs from day 21 to 35 of age (p > 0.05). Metagenomic analysis using 16S rRNA sequencing showed that the LNK1 group maintained a diverse and balanced gut microbiota, characterized by increased Firmicutes and reduced Proteobacteria. In contrast, the APEC group exhibited reduced diversity and dominance of Escherichia-Shigella (p < 0.001). These findings suggest Lc. NK1 could be a promising probiotic for enhancing gut health and growth performance in broilers, even under pathogenic challenges, offering a potential alternative to antibiotics in poultry production.

Genetic diversity and antibiogram of ESBL-producing Escherichia coli isolated from apparently healthy birds sold at two selected live bird markets in Nigeria

BACKGROUND

Live bird markets (LBMs) play a crucial role in the poultry value chain. However, there is a significant threat of antibiotic resistance development via this chain. This study aimed to characterise ESBL-producing Escherichia coli (E. coli) from cloacal samples of apparently healthy ducks and pigeons, determine their antibiotic resistance profile and carriage of ESBL genes.

METHODS AND RESULTS

Sasa and Molete LBMs were selected for this study. Three hundred and forty cloacal swabs (170 each from ducks and pigeons) were sampled and isolation of E. coli was done using the streak plate method. Resistance to a panel of 10 antibiotics was determined using the disc diffusion method and phenotypic ESBL production was carried out using the double disc synergy test (DDST). Detection of ESBL genes in the isolates was done using PCR amplification method. Out of 340 samples, 22.9% (n = 78) tested positive for E. coli. Among these, 38.5% (n = 30) were positive for ESBL production. The thirty ESBL-producing isolates showed varying level of resistance to the tested antibiotics, with the highest level of resistance observed to imipenem in both ducks and pigeons. Twenty of the ESBL producers showed multidrug-resistant phenotypes. blaCTX-M which was detected in 19 isolates (63.3%) was the most predominant ESBL gene among the isolates, while 15/30 (50.0%) carried blaSHV and 6/30 (20.0%) carried blaTEM. Thirteen (43.3%) and two (6.6%) isolates co-harboured two and all the three target ESBL genes, respectively.

CONCLUSIONS

This study has shown that LBMs in Ibadan are a repository of multidrug-resistant and ESBL-producing E. coli, hence urgent measures need to be taken to monitor and control the use of antibiotics in LBMs to mitigate this risk.

Plant Diversity Reduces the Risk of Antibiotic Resistance Genes in Agroecosystems

Despite advances in dispersal mechanisms and risk assessment of antibiotic resistance genes (ARGs), how plants influence ARG contamination in agricultural soils remains underexplored. Here, the impacts of plant species and diversity on ARGs and mobile genetic elements (MGEs) in three agricultural soils are comprehensively investigated in a pot experiment. The results indicate that increased plant diversity reduces ARGs and MGEs abundance by 19.2%-51.2%, whereas plant species exhibit inconsistent and soil-dependent effects. Potential bacterial hosts harboring abundant ARGs have greater relative abundance than nonhosts, and both their richness and cumulative relative abundance are reduced by plant diversity. Notably, hosts inhibited by plant diversity present a greater relative abundance than the other hosts. The enriched compounds in root exudates due to plant diversity play a more important role in the metabolic network and contribute to rebalancing of the abundance of potential hosts and nonhosts. An independent test using pure organics reveals that higher resource diversity, resulting from increased plant diversity, reduces the relative abundance and mobility of abundant and high-risk ARGs. This study highlights the resource-mediated mitigation of the risks posed by ARG contamination and indicates that ensuring plant and resource diversity is a promising strategy for controlling ARGs in agroecosystems.

Ontogenetic Analysis of Chelonus formosanus and Diversity of Its Internal Microbiota

Chelonus formosanus is a parasitic wasp capable of parasitizing various Noctuidae pests, including the highly invasive Spodoptera frugiperda, and it demonstrates strong pest control potential. Both egg and larval stages primarily occur within the host organism, and the total developmental time from egg to adult is approximately 19.62 days. To investigate the microbial communities at different stages, we performed 16S rDNA sequencing (V1-V9 region) using PacBio sequencing and identified 404 bacterial species belonging to 61 classes, 116 orders, 182 families, and 308 genera across larval, pupal, female, and male adult stages. Bacterial diversity and richness varied across the stages, with Enterobacter and Enterococcus dominating in larvae and pupae and Pseudomonas emerging as dominant in female adults. In contrast, male adults predominantly resided with Ralstonia and Achromobacter. The predicted functions of bacteria within C. formosanus at different developmental stages are predominantly marked by the high abundance of metabolic pathways. This study provides a comprehensive understanding of the morphology of C. formosanus and contributes to the practical control of host pests. Additionally, our findings preliminarily characterized the microbial community of various developmental stages, laying the groundwork for its functional study.

Comparative analysis of antibiotic resistance genes between fresh pig manure and composted pig manure in winter, China

Antibiotic resistance is a critical global public health issue. The gut microbiome acts as a reservoir for numerous antibiotic resistance genes (ARGs), which influence both existing and future microbial populations within a community or ecosystem. However, the differences in ARG expression between fresh and composted feces remain poorly understood. In this study, we collected eight samples from a farm in Kaifeng City, China, comprising both fresh and composted pig manure. Using a high-throughput quantitative PCR array, we analyzed differences in ARG expression between these two types of manure. Our findings revealed significant differences in ARG profiles, as demonstrated by principal coordinate analysis (PCoA). Further analysis identified 39 ARGs (log2FC > 1, p < 0.05) in composted pig manure, with 25 genes downregulated and 14 upregulated. Notably, tetB-01, blaOCH, and blaOXY were the most abundant in composted pig manure compared to fresh manure. Additionally, 16S rRNA species profiling revealed that the composting process significantly altered the microbial community structure, with an increased abundance of Firmicutes and a decreased abundance of Bacteroidetes in composted pig manure. In summary, composting substantially transforms both the microbial community structure and the ARG profile in pig manure, underscoring its potential role in modulating the dynamics of ARGs in agricultural environments.

Prevalence and dynamics of antimicrobial resistance in pioneer and developing Arctic soils

Antimicrobial resistance (AMR) in soil is an ancient phenomenon with widespread spatial presence in terrestrial ecosystems. However, the natural processes shaping the temporal dissemination of AMR in soils are not well understood. We aimed to determine whether, how, and why AMR varies with soil age in recently deglaciated pioneer and developing Arctic soils using a space-for-time approach. Specifically, we assess how the magnitude and spread of AMR changes with soil development stages, including antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and antibiotic-resistant bacteria (ARB). We showed that ARGs, MGEs, and ARB are present, and exhibit a non-uniform distribution in the developing soils. Their abundance generally increases with soil age but at different rates overall and across different glacier forefields. Our analyses suggest a strong positive relationship between soil age and ARGs and ARB, which we attribute to increased competition between microbes in older soils. We also observed a strong negative relationship between soil age and ARG diversity mediated by soil organic matter - suggesting facilitation due to the alleviation of nutrient limitation. These contrasting results suggest that both competition and facilitation can regulate AMR spread through time in the Arctic, but competition might be the stronger determinant of AMR spread.

Pasteurized waste milk vs. milk replacer at the same crude protein:metabolizable energy ratio with different energy sources (fat vs. lactose) to pre-weaning Holstein calves: Effects on growth performance, feeding behavior, and health

The improved growth performance of calves at weaning results from an effective pre-weaning feeding strategy. The type and pasteurization process of liquid feed are among the most variable feeding practices affecting calves' growth and health. In previous studies that compared waste milk (WM) vs. milk replacer (MR), little consideration has been given to the variations in chemical composition and feeding behavior between them, and there has been a lack of justification for the crude protein: metabolizable energy (CP:ME) ratio adopted. Hence, this study aimed to evaluate the effects of feeding pasteurized WM or MR differing in energy source (fat vs. lactose, respectively) with similar CP:ME ratio on intake, growth, feeding behavior, and health of newborn Holstein calves. Thirty-two male calves (4-d-old; 40.0 ± 0.58 kg BW) were assigned to the trial and randomly allocated to each liquid feed diet (WM or MR). Calves were housed in individual pens with free access to starter feed and fresh water. Calves were weaned on d 61 and assessed until d 101 as the postweaning period. WM-fed calves had greater total nutrient intake (DM, CP, EE, and ME), weight gain, final BW, skeletal growth parameters, and feed efficiency (d 30). Calves WM-fed sorted less against particles retained on the 2.36-mm sieve but more against particles retained on the sieve of 0.6 mm. In WM-fed calves, the sorting index decreased for feedstuff retaining on the bottom pan compared with MR-fed calves. Irrespective of the type of the liquid feed, all calves sorted for particles retaining on the sieve of 4.75 mm and the bottom pan, and against the particles that were retained on the sieves of 2.36- (MR-fed calves only), 1.18- and 0.6-mm. Starter feed nutrient intake and particle size intake from the sieves of 4.75-, 2.36-, and 1.18-mm increased in WM- vs. MR-fed calves. Eating rate and meal size but not meal frequency and length were greater in WM-fed calves, leading to higher pre- and post-weaning starter feed intake. Calves WM-fed spent less time eating and standing but more time ruminating and lying than MR-fed calves. Calves WM-fed had a lower likelihood of having elevated general appearance (score ≥2; hazard ratio = 2.79), diarrhea (score ≥3; hazard ratio = 1.35), and pneumonia (hazard ratio = 4.77). Calves WM-fed experienced shorter days with elevated general appearance, diarrhea, and pneumonia. Overall, feeding WM led to increased starter feed intake by boosting the eating rate and meal size, promoting greater growth than MR. Additionally, compared with MR, WM feeding increased time spent ruminating and lying and reduced susceptibility to diarrhea and pneumonia.

Deciphering the endomicrobiome of Podophyllum hexandrum to reveal the endophytic bacterial-association of in-planta podophyllotoxin biosynthesis

Understanding the change in plant-associated microbial diversity and secondary metabolite biosynthesis in medicinal plants due to their cultivation in non-natural habitat (NNH) is important to maintain their therapeutic importance. Here, the bacterial endomicrobiome of Podophyllum hexandrum plants of natural habitat (NH; Kardang and Triloknath locations) and NNH (Palampur location) was identified and its association with the biosynthesis of podophyllotoxin (PTOX) was revealed. Rhizomes (source of PTOX) of plants of NH had highest endophytic bacterial diversity compared to NNH-plants. Presence of plant-location and tissue-specific distinct and common taxa were also identified. Acinetobacter, Ralstonia and Pseudomonas were identified as core taxa, present in plants of both NH and NNH. Predictive functional analysis of endophytic communities revealed abundant presence of genes encoding initial enzymes of PTOX biosynthesis and plant growth promotion in the rhizomes and roots of Kardang locations. Higher accumulations of secondary metabolites such as PTOX (2.78 and 2.11 folds in Kardang and Triloknath rhizomes, respectively; 1.48 and 1.71 fold in Kardang and Triloknath roots, respectively), Picropodophyllotoxin (3.08 fold in Kardang rhizomes), Quercetin (1.65 fold in Kardang and 1.32 fold in Triloknath rhizomes; 3.07-fold in Kardang and 1.60 fold in Triloknath roots) and Kaempferol (1.66 and 1.24-fold in Kardang and Triloknath rhizomes, respectively; 2.91 and 1.94-fold in Kardang and Triloknath roots, respectively) were also found in NH compared to NNH. This study provides novel insight into the change in the endomicrobiome of NH and NNH-plants and their correlation to secondary metabolites biosynthesis, and that must be considered for cultivation practices.

Dietary supplementation with compound microecological preparations: effects on the production performance and gut microbiota of lactating female rabbits and their litters

Early weaning is frequently accompanied by a significant increase in diarrhea and mortality rates, which reduces rabbits' performance. Although antibiotics can reduce pathogenic bacteria, they also harm beneficial microorganisms and disrupt the normal intestinal microbiota balance. In order to find non-residue and non-toxic alternatives to antibiotics to ensure the safety of animal products, we conducted a study on the effect of compound microecological preparations supplementation on lactating female rabbits and their offspring. A total of 60 female rabbits were randomly assigned to four groups: CON, supplemented with probiotics at 3, 6, and 9 g/female rabbit/day from day 24 of gestation until weaning. We observed that probiotics supplementation significantly enhanced production performance (P < 0.05), immune and antioxidant function (P < 0.05), as well as intestinal flora composition in lactating rabbits and their offspring. Notably, compared with the control group, the experimental group exhibited a 19.23%, 44.22%, and 24.57% increase in milk yield (P = 0.002). Regarding rabbit growth performance, the average body weight of young rabbits in the experimental group showed a significant increase of 3.59%, 10.22%, and 6.74% at day 35 (P = 0.022), whereas the average daily gain (ADG) of rabbits aged between 21 and 35 days was significantly elevated by 4.94%, 17.06%, and 6.28% in the experimental group (P < 0.001). In conclusion, probiotics supplementation can significantly enhance lactation performance, promote growth and disease resistance in rabbits, as well as improve intestinal health when administered at a dosage of 6 g/day. Moreover, the limited sample size in this study may hinder the detection of subtle effects, and augmenting the sample size will bolster the reliability of the study findings.

IMPORTANCE

The intestinal environment of rabbits is fragile and susceptible to environmental influences, leading to inflammatory intestinal diseases. Adding antibiotics to rabbit feed can achieve the effect of preventing and treating inflammation, which can also lead to the imbalance of the gut microbiota and residual antibiotics in agricultural products. Composite probiotics are live microbial feed additives composed of various ratios of probiotics and have become the most promising alternative to antibiotics due to their residue-free and non-toxic properties. The aim of this study was to investigate the impact of compound probiotics on lactating female rabbits and their offspring. Our findings highlight the potential of compound microecological preparations as an effective strategy for enhancing lactation performance, immune function, and antioxidant capacity in rabbits. The supplementation of probiotics through rabbit milk offers a promising approach to optimize the growth and health outcomes of newborn rabbits.

Fungi in the Gut Microbiota: Interactions, Homeostasis, and Host Physiology

The mammalian gastrointestinal tract is a stage for dynamic inter-kingdom interactions among bacteria, fungi, viruses, and protozoa, which collectively shape the gut micro-ecology and influence host physiology. Despite being a modest fraction, the fungal community, also referred to as mycobiota, represents a critical component of the gut microbiota. Emerging evidence suggests that fungi act as early colonizers of the intestine, exerting a lasting influence on gut development. Meanwhile, the composition of the mycobiota is influenced by multiple factors, with diet, nutrition, drug use (e.g., antimicrobials), and physical condition standing as primary drivers. During its establishment, the mycobiota forms both antagonistic and synergistic relationships with bacterial communities within the host. For instance, intestinal fungi can inhibit bacterial colonization by producing alcohol, while certain bacterial pathogens exploit fungal iron carriers to enhance their growth. However, the regulatory mechanisms governing these complex interactions remain poorly understood. In this review, we first introduce the methodologies for studying the microbiota, then address the significance of the mycobiota in the mammalian intestine, especially during weaning when all 'primary drivers' change, and, finally, discuss interactions between fungi and bacteria under various influencing factors. Our review aims to shed light on the complex inter-kingdom dynamics between fungi and bacteria in gut homeostasis and provide insights into how they can be better understood and managed to improve host health and disease outcomes.

Concordance in molecular methods for detection of antimicrobial resistance: A cross sectional study of the influent to a wastewater plant

Methods that are used to characterise microbiomes and antimicrobial resistance genes (ARGs) in wastewater are not standardised. We used shotgun metagenomic sequencing (SM-Seq), RNA sequencing (RNA-seq) and targeted qPCR to compare microbial and ARG diversity in the influent to a municipal wastewater treatment plant in Australia. ARGs were annotated with CARD-RGI and MEGARes databases, and bacterial diversity was characterised by 16S rRNA gene sequencing and SM-Seq, with species annotation in SILVA/GreenGenes databases or Kraken2 and the NCBI nucleotide database respectively. CARD and MEGARes identified evenly distributed ARG profiles but MEGARes detected a richer array of ARGs (richness = 475 vs 320). Qualitatively, ARGs encoding for aminoglycoside, macrolide-lincosamide-streptogramin and multidrug resistance were the most abundant in all examined databases. RNA-seq detected only 32 % of ARGs identified by SM-Seq, but there was concordance in the qualitative identification of aminoglycoside, macrolide-lincosamide, phenicol, sulfonamide and multidrug resistance by SM-Seq and RNA-seq. qPCR confirmed the detection of some ARGs, including OXA, VEB and EREB, that were identified by SM-Seq and RNA-seq in the influent. For bacteria, SM-Seq or 16S rRNA gene sequencing were equally effective in population profiling at phyla or class level. However, SM-Seq identified a significantly higher species richness (richness = 15,000 vs 3750). These results demonstrate that SM-Seq with gene annotation in CARD and MEGARes are equally sufficient for surveillance of antimicrobial resistance in wastewater. For more precise ARG identification and quantification however, MEGARes presented a better resolution. The functionality of detected ARGs was not confirmed, but general agreement on the putative phenotypic resistance profile by antimicrobial class was observed between RNA-Seq and SM-Seq.

High Concentrations of Tilmicosin Promote the Spread of Multidrug Resistance Gene tolC in the Pig Gut Microbiome Through Mobile Genetic Elements

The impact of antibiotic therapy on the spread of antibiotic resistance genes (ARGs) and its relationship to gut microbiota remains unclear. This study investigated changes in ARGs, mobile genetic elements (MGEs), and gut microbial composition following tilmicosin administration in pigs. Thirty pigs were randomly divided into control (CK), low-concentration (0.2 g/kg; L), and high-concentration (0.4 g/kg; H) groups. Tilmicosin concentration in manure peaked on day 16 of dosing and dropped below detectable levels by day 13 of the withdrawal period. While tilmicosin did not significantly affect the total abundance of macrolide resistance genes (MRGs) (p > 0.05), it significantly increased the abundance of the multidrug resistance gene tolC in the H group compared with the L and CK groups during the withdrawal period (p < 0.05). This increase was associated with a coincidental rise in the abundance of MGEs (e.g., int1 and int2) and the growth of potential tolC-hosting bacteria such as Paenalcaligenes and Proteiniclasticum. Redundancy analysis showed gut microbial composition as the primary driver of MRG abundance, with MGEs, tilmicosin concentration, and manure physicochemical properties playing secondary roles. These findings suggest that high-dose tilmicosin may alter the gut microbiota and promote ARG spread via MGE-mediated transfer.

Comprehensive effects of tea branch biochar on antibiotic resistance profiles and C/N/S cycling in the compost microbiota of animal manure

The comprehensive effects of exogenous additives on microbial-driven antibiotic resistance profiles and C/N/S conversion in animal manure composting remains uncertain. This study examined whether tea branch biochar could regulate the microflora involved in antibiotic resistance and C/N/S conversion during pig and chicken manure composting. Compared with the control treatment, biochar addition prolonged the high-temperature period (>55 °C) for 1-2 days and raised the maximum temperature in chicken manure composting. Moreover, biochar addition reduced the prevalence of antibiotic resistance genes (ARGs) in both pig and chicken manure composting by up to 30 %, targeting various types of ARGs such as peptide, phenicol, and diaminopyrimidines. Additionally, the compost microbiota exhibited the overlaps of C/N/S conversion functions. Luteimonas (Xanthomonadaceae) was identified as a dominant bacterium responsible for C/N/S conversion in both pig and chicken manure composting, while also acting as a potential ARG carrier. Thus, Luteimonas is crucial in shaping antibiotic resistance profiles and C/N/S cycling in animal manure composting, indicating its role as a keystone genus. These findings suggest that tea branch biochar can mitigate the spread of ARGs from animal manure, as well as enhance nutrient cycling and compost quality.

Interaction Between Liver Metabolism and Gut Short-Chain Fatty Acids via Liver-Gut Axis Affects Body Weight in Lambs

The gut-liver axis and its interactions are essential for host physiology. Thus, we examined the jejunal microbiota, fermentation parameters, digestive enzymes, morphology, and liver metabolic profiles in different growth development lambs to investigate the liver-gut axis's role in their development. One hundred male Hu lambs of similar birth weight and age were raised under the same conditions until they reached 180 days of age. Subsequently, the eight lambs with the highest (HADG) and lowest (LADG) average daily weight gains were slaughtered for index assessment. The study indicates that the body weight, carcass weight, propanoic acid, butyric acid, propanoic acid ratio, butyric acid ratio, and digestive enzymes (beta-glucosidase, microcrystalline cellulase, xylanase, and carboxymethyl cellulase) were significantly higher in HDAG lambs than in LADG lambs (p < 0.05). Additionally, there were no significant differences in the jejunal microbiota's structure and function among lambs at different growth development stages (p > 0.05). Overall, our analysis revealed that HADG lambs compared to LADG lambs exhibited an up-regulation of metabolites (such as spermine, cholic acid, succinic acid, betaine, etc.) that were positively correlated with the butyric acid ratio, propanoic acid ratio, propanoic acid, xylanase, microcrystalline cellulase, beta-glucosidase, amylase, carboxymethyl cellulase, carcass weight, and body weight, while these metabolites were negatively correlated with the kidney, acetic acid, acetic acid/ propanoic acid, and acetic acid ratio. Furthermore, there was a significant correlation between liver metabolism and jejunal microbiota. This study revealed significant differences in hepatic metabolites and jejunal fermentation among lambs at different growth stages, which may inform targeted regulation strategies to enhance lamb productivity.

Impacts of soil type on the temporal dynamics of antibiotic resistance gene profiles following application of composted manure

Farmland application of composted manure is associated with a risk of dissemination of antibiotic resistance genes (ARGs) in agricultural soils. However, the impact of soil type on the temporal dynamics of ARGs in agricultural soil remains largely unclear. The aims of this study were to study the persistence of composted manure-derived ARGs in six soil types representative for Chinese agriculture and to explore the underlying environmental drivers of soil ARG profiles in a controlled greenhouse experiment. Temporal dynamics of manure-derived ARGs was strongly affected by soil type. High persistence of fertilizer-derived ARGs was evident in red soil, yellow soil and sierozem soil, while a rapid decrease to near pre-fertilization levels (low persistence) was observed in yellow-brown soil, black soil and brown earth soil. The distribution of ARGs was linked to soil properties such as soil texture, pH and concentrations of heavy metals. More complex co-occurrence networks of ARGs and bacteria in red soil, yellow soil, and sierozem soil suggested a higher dissemination potential, which was consistent with the significantly increased abundance of MGEs in these three types of soils. Our findings highlight the necessity for developing tailored fertilization strategies for different soil types to mitigate environmental dissemination of ARGs.

A comprehensive review of antibiotic resistance gene contamination in agriculture: Challenges and AI-driven solutions

Since their discovery, the prolonged and widespread use of antibiotics in veterinary and agricultural production has led to numerous problems, particularly the emergence and spread of antibiotic-resistant bacteria (ARB). In addition, other anthropogenic factors accelerate the horizontal transfer of antibiotic resistance genes (ARGs) and amplify their impact. In agricultural environments, animals, manure, and wastewater are the vectors of ARGs that facilitate their spread to the environment and humans via animal products, water, and other environmental pathways. Therefore, this review comprehensively analyzed the current status, removal methods, and future directions of ARGs on farms. This article 1) investigates the origins of ARGs on farms, the pathways and mechanisms of their spread to surrounding environments, and various strategies to mitigate their spread; 2) determines the multiple factors influencing the abundance of ARGs on farms, the pathways through which ARGs spread from farms to the environment, and the effects and mechanisms of non-antibiotic factors on the spread of ARGs; 3) explores methods for controlling ARGs in farm wastes; and 4) provides a comprehensive summary and integration of research across various fields, proposing that in modern smart farms, emerging technologies can be integrated through artificial intelligence to control or even eliminate ARGs. Moreover, challenges and future research directions for controlling ARGs on farms are suggested.

From grasslands to genes: exploring the major microbial drivers of antibiotic-resistance in microhabitats under persistent overgrazing

BACKGROUND

The extensive use of antibiotics in the global livestock industry in recent decades has accelerated the accumulation and dissemination of antibiotic-resistance genes (ARGs) within terrestrial ecosystems. This occurs due to the limited absorption of most antibiotics, leading to their release into the environment through feces and urine. This poses a significant threat to both the environment and human health. However, the response of antibiotic-resistant microorganisms and their ARGs in grasslands to prolonged grazing, as well as the primary microbial taxa driving the ARG distribution, remain poorly understood, especially within various microhabitats. In this study, we characterized ARGs in the phyllosphere, litter, and soil after decades of livestock grazing in a meadow steppe. We particularly focused on identifying the major members of the microbial community influencing ARGs and the distinction between microbial generalists and specialists.

RESULTS

Our findings indicate that a core set of ARGs accounted for 90% of the abundance in this plant-soil ecosystem. While the soil exhibited the highest ARG abundance, the phyllosphere, and litter displayed higher ARG diversity and diverse distribution patterns after overgrazing. Grazing increased ARG abundance by elevating the proportion of core ARGs and suppressing stochastic ARGs in the phyllosphere and litter, while it had little effect on the ARGs in the soil. Additionally, microbial generalist abundance increased, but specialist abundance decreased in the phyllosphere and litter, with no effect in the soil, under grazed conditions. Ultimately, microbial microhabitats and grazing influenced ARG community characteristics through direct (i.e., feces and other exogenous ARG input) and indirect (i.e., trampling and selective feeding) effects on nutrient availability, microbial community composition, and mobile genetic elements. The generalist community, with its broad ecological niches and phylogenetic composition, made the most significant contribution to the ARG characteristics.

CONCLUSIONS

This study underscores the impact of environmental disturbances on the distributional patterns of ARGs in ecosystems, mediated by the regulation of microbial generalized species. These insights enhance our understanding of microbial control over ARGs and facilitate predictions regarding the dynamics and risk of ARGs in diverse ecological niches subjected to anthropogenic disturbances. Video Abstract.

Trajectory of antibiotic resistome response to antibiotics gradients: A comparative study from pharmaceutical and associated wastewater treatment plants to receiving river

Pharmaceutical wastewater often contains significant levels of antibiotic residues, which continuously induce and promote antibiotic resistance during the sewage treatment process. However, the specific impact of antibiotics on the emergence of antibiotic resistance genes (ARGs), microbiomes, and mobile genetic elements (MGEs), as well as the dose-response relationship remain unclear. Herein, through metagenomic sequencing and analysis, we investigated the fate, transmission, and associated risk of ARGs over a ten-year period of exposure to a gradient of sulfonamide antibiotics at a pharmaceutical wastewater treatment plant (PWWTP), an associated wastewater treatment plant (WWTP), and the receiving river. Through abundance comparison and principal co-ordinates analysis (PCoA), our results revealed distinct ARG, microbiome, and MGE profiles across different antibiotic concentrations. Notably, there was a decreasing trend in the abundance of ARGs and MGEs as the antibiotic concentrations were attenuated (p < 0.05). Further partial least squares path modeling analysis, Procrustes analysis and network analysis indicated that variation in MGEs and microbiomes were the driving forces behind the distribution of ARGs. Based on these findings, we proposed an antibiotic-microbiome-MGE-ARG dissemination paradigm, in which integrons as key drivers were closely associated with prevalent ARGs such as sul1, sul2, and aadA. With a focus on human pathogenic bacteria and the associated health risks of ARGs, we conducted pathogen source analysis and calculated the antibiotic resistome risk index (ARRI). Our findings highlighted potential risks associated with the transition from PWWTP to WWTP, raising concerns regarding risk amplification due to the mixed treatment of antibiotic-laden industrial wastewater and domestic sewage. Overall, the results of our study provide valuable information for optimizing wastewater treatment practices to better manage antibiotic resistance.

Traditionally produced tempeh harbors more diverse bacteria with more putative health-promoting properties than industrially produced tempeh

In recent years, there has been a significant shift towards industrialization in food production, resulting in the implementation of higher hygiene standards globally. Our study focused on examining the impact of hygiene standards on tempeh, a popular Rhizopus-based fermented soybean product native to Indonesia, and now famous around the world. We observed that tempeh produced with standardized hygiene measures exhibited a microbiome with comparable bacterial abundances but a markedly different community structure and function than traditionally produced tempeh. In detail, we found a decreased bacterial abundance of lactobacilli and enterobacteria, bacterial diversity, different indicator taxa, and significantly changed community structure in industrial tempeh. A similar picture was found for functional analysis: the quantity of bacterial genes was similar but qualitative changes were found for genes associated with human health. The resistome of tempeh varied based on its microbiome composition. The higher number of antimicrobial resistance genes in tempeh produced without standardized hygiene measures mainly belong to multidrug efflux pumps known to occur in plant-based food. Our findings were confirmed by functional insights into genomes and metagenome-assembled genomes from the dominant bacteria, e.g. Leuconostoc, Limosilactobacillus, Lactobacillus, Enterococcus, Paenibacillus, Azotobacter and Enterobacter. They harboured an impressive spectrum of genes important for human health, e.g. for production of vitamin B1, B7, B12, and K, iron and zinc transport systems and short chain fatty acid production. In conclusion, industrially produced tempeh harbours a less diverse microbiome than the traditional one. Although this ensures production at large scales as well as biosafety, in the long-term it can lead to potential effects for human gut health.

Aspirin altered antibiotic resistance genes response to sulfonamide in the gut microbiome of zebrafish

Pharmaceuticals are widespread in aquatic environments and might contribute to the prevalence of antibiotic resistance. However, the co-effect of antibiotics and non-antibiotic pharmaceuticals on the gut microbiome of fish is poorly understood. In this study, we characterized the variation of the zebrafish gut microbiome and resistome after exposure to sulfamethoxazole (SMX) and aspirin under different treatments. SMX contributed to the significant increase in the antibiotic resistance genes (ARGs) richness and abundance with 46 unique ARGs and five mobile genetic elements (MGEs) detected. Combined exposure to SMX and aspirin enriched total ARGs abundance and rearranged microbiota under short-term exposure. Exposure time was more responsible for resistome and the gut microbiome than exposure concentrations. Perturbation of the gut microbiome contributed to the functional variation related to RNA processing and modification, cell motility, signal transduction mechanisms, and defense mechanisms. A strong significant positive correlation (R = 0.8955, p < 0.001) was observed between total ARGs and MGEs regardless of different treatments revealing the key role of MGEs in ARGs transmission. Network analysis indicated most of the potential ARGs host bacteria belonged to Proteobacteria. Our study suggested that co-occurrence of non-antibiotics and antibiotics could accelerate the spread of ARGs in gut microbial communities and MGEs played a key role.

Occurrence and distribution of antibiotic resistance genes in urban rivers with black-odor water of Harbin, China

Antibiotic resistance gene contamination in polluted rivers remains a widely acknowledged environmental issue. This study focused on investigating the contamination conditions of antibiotic resistance genes (ARGs) in Harbin's urban black-odor rivers, specifically Dongfeng Ditch and Hejia Ditch. The research employed a SmartChip Real-Time PCR System to explore the types, abundance, and distribution of ARGs in diverse habitats, such as surface water and sediment. Additionally, the study examined the correlation of ARGs with mobile genetic elements (MGEs) and various environmental factors. It was found that antibiotic resistance genes were prevalent in both water and sediment within the black-odor ditches. The dominant types of ARGs identified included aminoglycoside, sulfonamide, multidrug-resistant, and β-lactam ARGs. Notably, the top four ARGs, in terms of relative abundance, were sul1, fox5, qacEdelta1-01 and aadA1. Most categories of ARGs have significant positive connections with MGEs, indicating that the enrichment and spreading of ARGs in rivers are closely related to MGEs. Based on the correlation analysis, it is found that environmental factors such as dissolved oxygen (DO), ammonia nitrogen (NH4-N), and phosphate (PO4-P) played a substantial role in influencing the variations observed in ARGs. By employing a risk assessment framework based on the human association, host pathogenicity, and mobility of ARGs, the identification of seven high-risk ARGs was achieved. In addition, it is important to assess the environmental risk of ARGs from multiple perspectives (abundance,detection rateand mobility). This study provides a significant reference regarding the presence of ARGs contamination in urban inland black-odor rivers, essential for assessing the health risks associated with ARGs and devising strategies to mitigate the threat of antibiotic resistance.

Unveiling symbiotic bacterial communities in insects feeding on the latex-rich plant Ficus microcarpa

The diversity and health of insects that feed on plants are closely related to their mutualistic symbionts and host plants. These symbiotic partners significantly influence various metabolic activities in these insects. However, the symbiotic bacterial community of toxic plant feeders still needs further characterisation. This study aims to unravel bacterial communities associated with the different species of insect representing three insect orders: Thysanoptera, Hemiptera, and Lepidoptera, along with their predicted functional role, which exclusively feeds on latex-rich plant species Ficus microcarpa. By using 16S rRNA gene high-throughput sequencing, the analysis was able to define the major alignment of the bacterial population, primarily comprising Proteobacteria, Firmicutes, Bacteroidota, Actinobacteriota, and Acidobacteriota. Significant differences in symbiotic organisms between three insect groups were discovered by the study: hemipterans had Burkholderia and Buchnera, and lepidopterans had Acinetobacter. At the same time, Pseudomonas was detected in high abundance in both lepidopteran and thysanopteran insects. Furthermore, these symbionts exhibit consistent core functions, potentially explaining how different insects can consume the same host plant. The identified core functions of symbionts open avenues for innovative approaches in utilising these relationships to develop environment-friendly solutions for pest control, with broader implications for agriculture and environmental conservation.

Temporal variation characteristics of microbial aerosols in the goose house environment

1. Preventing disease is important in poultry production systems, but this has mainly been studied in chickens. The aim of this study is to explore the impact of microbial aerosols in intensive goose house environments.2. To evaluate the environmental quality of geese housing, fine particulate matter (PM2.5) was collected using an ambient air particulate matter sampler. High-throughput sequencing was used to analyse bacterial diversity and relative abundance. Results showed that the number of general and operational taxonomic units (OTUs) were 1,578 and 19 112 in all PM2.5 samples. Firmicutes, Bacteroidota, Proteobacteria, Acidobacterota were the four most abundant phyla in PM2.5.3. Compared with bacterial phyla in the PM2.5 from chicken houses, those in the genus Acidobacterota were increased in goose housing. There are various genera of bacteria present in PM2.5, and their composition was similar across different samples. No significant change was observed in the diversity of microbiota in the PM2.5, although multiple pathogenic bacteria were detected.4. A prediction function showed that a variety of bacterial phyla correlated positively with the human diseases.5. In summary, the microbial aerosols in the goose shed pose significant risks to the health of the geese. Regular monitoring of the composition of microbial aerosols is important for the healthy growth of geese and disease prevention and control.

Effects of mulch films with different thicknesses on the microbial community of tobacco rhizosphere soil in Yunnan laterite

The mulch film (MF) management model of the agricultural field affects the physical and chemical properties of soil (PCPS) and the structure of the microorganism community; however, studies on the relationship between the rhizosphere microorganism community structure and the thickness of MF are still limited. To understand the interactions among the MF thickness, PCPS, and rhizosphere microorganism, a study was conducted by using an integrated metagenomic strategy, where tobacco rhizosphere soil was treated with four commonly representative and used thicknesses of MFs (0.004, 0.006, 0.008, and 0.010 mm) in Yunnan laterite. The results showed that agronomic traits such as the tobacco plant height (TPH), leaf number (LN), fresh leaf weight (FLW), and dry leaf weight (DLW) were significantly (p < 0.01) improved in the field mulched with the thickest film (0.010 mm) compared with the exposed field (CK), and there was a 6.81 and 5.54% increase in the FLW and TPH, separately. The correlation analyses revealed a significant positive correlation of the MF thickness with the soil water content (SWC), soil organic matter (SOM), total nitrogen (TN), available nitrogen (AN), total phosphorus (TP), and available phosphorus (AP; all p < 0.01), while the MF thickness was negatively correlated with the soil temperature (ST; p < 0.01). In addition, the community structure of the rhizosphere soil bacteria was significantly changed overall by the MF thickness, which also interfered with the function of the rhizosphere soil bacteria. The correlation analyses also showed that the abundance of Bradyrhizobium and Nitrospira was positively correlated with the MF thickness, while the abundance of Sphinsinomonas and Massilia was negatively correlated with it. This indicated that with the increase of the MF thickness, the ability of the rhizosphere soil to utilize N and remove harmful molecules was strengthened, while the capacity of the rhizosphere soil to degrade pollutants was greatly reduced. These findings provide additional insights into the potential risks of the application of different thicknesses of MFs, particularly concerning the PCPS and soil microbial communities.

Opposite Effects of Planting on Antibiotic Resistomes in Rhizosphere Soil with Different Sulfamethoxazole Levels

Achieving consensus about the rhizosphere effect on soil antibiotic resistomes is challenging due to the variability in antibiotic concentrations, sources, and the elusory underlying mechanisms. Here, we characterized the antibiotic resistomes in both the rhizosphere and bulk soils of soybean plants grown in environments with varying levels of antibiotic contamination, using sulfamethoxazole (SMX) as a model compound. We also investigated the factors influencing resistome profiles. Soybean cultivation altered the structure of antibiotic-resistant genes (ARGs) and increased their absolute abundance. However, the rhizosphere effect on the relative abundance of ARGs was dependent on SMX concentrations. At low SMX levels, the rhizosphere effect was characterized by the inhibition of antibiotic-resistant bacteria (ARBs) and the promotion of sensitive bacteria. In contrast, at high SMX levels, the rhizosphere promoted the growth of ARBs and facilitated horizontal gene transfer of ARGs. This novel mechanism provides new insights into accurately assessing the rhizosphere effect on soil antibiotic resistomes.

Biofilms in plastisphere from freshwater wetlands: Biofilm formation, bacterial community assembly, and biogeochemical cycles

Microorganisms can colonize to the surface of microplastics (MPs) to form biofilms, termed "plastisphere", which could significantly change their physiochemical properties and ecological roles. However, the biofilm characteristics and the deep mechanisms (interaction, assembly, and biogeochemical cycles) underlying plastisphere in wetlands currently lack a comprehensive perspective. In this study, in situ biofilm formation experiments were performed in a park with different types of wetlands to examine the plastisphere by extrinsic addition of PVC MPs in summer and winter, respectively. Results from the spectroscopic and microscopic analyses revealed that biofilms attached to the MPs in constructed forest wetlands contained the most abundant biomass and extracellular polymeric substances. Meanwhile, data from the high-throughput sequencing showed lower diversity in plastisphere compared with soil bacterial communities. Network analysis suggested a simple and unstable co-occurrence pattern in plastisphere, and the null model indicated increased deterministic process of heterogeneous selection for its community assembly. Based on the quantification of biogeochemical cycling genes by high-throughput qPCR, the relative abundances of genes involving in carbon degradation, carbon fixation, and denitrification were significantly higher in plastisphere than those of soil communities. This study greatly enhanced our understanding of biofilm formation and ecological effects of MPs in freshwater wetlands.

Deciphering the differences of bacterial communities between high- and low-productive wheat fields using high-throughput sequencing

Microbial communities have been demonstrated to be essential for healthy and productive soil ecosystems. However, an understanding of the relationship between soil microbial community and soil productivity levels is remarkably limited. In this study, bulk soil (BS), rhizosphere soil (RS), and root (R) samples from the historical high-productive (H) and low-productive (L) soil types of wheat in Hebei province of China were collected and analyzed by high-throughput sequencing. The study highlighted the richness, diversity, and structure of bacterial communities, along with the correlation networks among different bacterial genera. Significant differences in the bacterial community structure between samples of different soil types were observed. Compared with the low-productive soil type, the bacterial communities of samples from the high-productive soil type possessed high species richness, low species diversity, complex and stable networks, and a higher relative abundance of beneficial microbes, such as Pseudoxanthomonas, unclassified Vicinamibacteraceae, Lysobacter, Massilia, Pseudomonas, and Bacillus. Further analysis indicated that the differences were mainly driven by soil organic matter (SOM), available nitrogen (AN), and electrical conductivity (EC). Overall, the soil bacterial community is an important factor affecting soil health and crop production, which provides a theoretical basis for the targeted regulation of microbes in low-productivity soil types.

Efficient elimination of antibiotic resistome in livestock manure by semi-permeable membrane covered hyperthermophilic composting

Livestock manure is a hotspot for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and an important contributor to antibiotic resistance in non-clinical settings. This study investigated the effectiveness and potential mechanisms of a novel composting technology, semi-permeable membrane covered hyperthermophilic composting (smHTC), in removal of ARGs and MGEs in chicken manure. Results showed that smHTC was more efficient in removal of ARGs and MGEs (92% and 93%) compared to conventional thermophilic composting (cTC) (76% and 92%). The efficient removal in smHTC is attributed to direct or indirect negative effects caused by the high temperature, including reducing the involvement of bio-available heavy metals (HMs) in co-selection processes of antibiotic resistance, decreasing the bacterial abundance and diversity, suppressing the horizontal gene transfer and killing potential ARGs hosts. Overall, smHTC can efficiently remove the resistome in livestock manure, reducing the risk to crops and humans from ARGs residues in compost products.

The distribution and key influential factors of antibiotic resistance genes in agricultural soils polluted by multiple heavy metals

Due to anthropogenic activities such as mining, several agricultural soils are polluted by multiple heavy metals. However, it is still unclear whether multiple heavy metals could affect the distribution of antibiotic resistance genes (ARGs), and how metals affect ARGs. To understand ARGs' distribution in heavy metal-polluted soils, we chose soils contaminated by different types and contents of heavy metals to determine the ARGs' number and abundance through high-throughput quantitative real-time PCR (HT-qPCR) in this study. Additionally, the factors affecting ARGs' distribution, such as soil properties, mobile genetic genes (MGEs), and bacterial communities, were explored. The results demonstrated that the sampled soils were primarily contaminated by Cd, As, Pb, and Zn, and the pollution load index (PLI) values of these metals ranged from 1.3 to 2.7, indicating a low to moderate degree of heavy metal contamination. The number and abundance of ARGs ranged from 44 to 113 and from 2.74 × 107 copies/g to 1.07 × 108 copies/g, respectively. Besides, abundant MGEs in soils, ranging from 1.84 × 106 copies/g to 5.82 × 106 copies/g, were observed. The pathway analysis suggested that MGEs were the most important factor directly affecting ARG abundance (0.89). Notably, heavy metals also affected the ARG abundance. Proteobacteria and Actinobacteria, the main heavy metal tolerant bacteria, were found to be the main hosts of ARGs through network analysis. ARG-carrying pathogens (ACPs) in agricultural soils were found to carry MGEs, indicating a high risk of dissemination. This study provided important information for understanding the ARGs' fate and also the key factors affecting ARGs' spread in multiple heavy metal-contaminated soils.

Fecal microbiota transplantation accelerates restoration of florfenicol-disturbed intestinal microbiota in a fish model

Antibiotic-induced dysbiosis in the fish gut causes significant adverse effects. We use fecal microbiota transplantation (FMT) to accelerate the restoration of florfenicol-perturbed intestinal microbiota in koi carp, identifying key bacterial populations and metabolites involved in the recovery process through microbiome and metabolome analyses. We demonstrate that florfenicol disrupts intestinal microbiota, reducing beneficial genera such as Lactobacillus, Bifidobacterium, Bacteroides, Romboutsia, and Faecalibacterium, and causing mucosal injuries. Key metabolites, including aromatic amino acids and glutathione-related compounds, are diminished. We show that FMT effectively restores microbial populations, repairs intestinal damage, and normalizes critical metabolites, while natural recovery is less effective. Spearman correlation analyses reveal strong associations between the identified bacterial genera and the levels of aromatic amino acids and glutathione-related metabolites. This study underscores the potential of FMT to counteract antibiotic-induced dysbiosis and maintain fish intestinal health. The restored microbiota and normalized metabolites provide a basis for developing personalized probiotic therapies for fish.

Gut microbiome perturbation and its correlation with tylosin pharmacokinetics in healthy and infected pigs

Tylosin, an antibiotic with a long history in treating respiratory bacterial infections, has unknown effects on the gut microbiota of healthy and infected pigs. The study aimed to investigate the effect of a therapeutic dose of tylosin on swine gut microbiota and explored the relationship between this effect and tylosin pharmacokinetics (PK). We also assessed whether changes in gut microbiota after tylosin administration differ between healthy animals (n = 7) and animals intranasally co-infected (n = 7) with Actinobacillus pleuropneumoniae and Pasteurella multocida. Both groups were intramuscularly administered with tylosin (20 mg/kg). The 16S rRNA gene analyses revealed a significantly lower species richness and diversity, after tylosin treatment, in the infected than the healthy pigs, with infected pigs having lower levels of Bacteroidetes and Firmicutes and higher levels of Proteobacteria. Greater tylosin exposure (greater area under curve (AUC) and maximum plasma concentration (Cmax), and slower elimination (longer terminal half-life, T1/2) were observed in healthy than infected pigs. Relative abundance of Lactobacillus, Oscillibacter, Prevotella, and Sporobacter was positively and significantly correlated with AUC and Cmax, whereas the abundance of Acinetobacter, Alishewanella, and Pseudomonas was positively and significantly correlated with T1/2 and mean residence time (MRT) of tylosin. Our findings, for the first time, demonstrated significant changes in swine gut microbiota after a single therapeutic dose of tylosin was administered, whereas the effect of these changes on tylosin PK was not evident.

Reduction in antimicrobial resistance in a watershed after closure of livestock farms

Natural environments play a crucial role in transmission of antimicrobial resistance (AMR). Development of methods to manage antibiotic resistance genes (ARGs) in natural environments are usually limited to the laboratory or field scale, partially due to the complex dynamics of transmission between different environmental compartments. Here, we conducted a nine-year longitudinal profiling of ARGs at a watershed scale, and provide evidence that restrictions on livestock farms near water bodies significantly reduced riverine ARG abundance. Substantial reductions were revealed in the relative abundance of genes conferring resistance to aminoglycosides (42%), MLSB (36%), multidrug (55%), tetracyclines (53%), and other gene categories (59%). Additionally, improvements in water quality were observed, with distinct changes in concentrations of dissolved reactive phosphorus, ammonium, nitrite, pH, and dissolved oxygen. Antibiotic residues and other pharmaceuticals and personal care products (PPCPs) maintain at a similarly low level. Microbial source tracking demonstrates a significant decrease in swine fecal indicators, while human fecal pollution remains unchanged. These results suggest that the reduction in ARGs was due to a substantial reduction in input of antibiotic resistant bacteria and genes from animal excreta. Our findings highlight the watershed as a living laboratory for understanding the dynamics of AMR, and for evaluating the efficacy of environmental regulations, with implications for reducing environmental risks associated with AMR on a global scale.

Penguin-Driven Dissemination and High Enrichment of Antibiotic Resistance Genes in Lake Sediments across Antarctica

Numerous penguins can propagate pathogens with antibiotic resistance genes (ARGs) into Antarctica. However, the effects of penguin dissemination on the lake ARGs still have received little attention via guano deposition. Here, we have profiled ARGs in ornithogenic sediments subject to penguin guano (OLS) and nonornithogenic sediments (NOLS) from 16 lakes across Antarctica. A total of 191 ARGs were detected in all sediment samples, with a much higher abundance and diversity in OLS than in NOLS. Surprisingly, highly diverse and abundant ARGs were found in the OLS with a detection frequency of >40% and an absolute abundance of (2.34 × 109)-(4.98 × 109) copies g-1, comparable to those in coastal estuarine sediments and pig farms. The strong correlations of identified resistance genes with penguin guano input amount, environmental factors, mobile genetic elements, and bacterial community, in conjunction with network and redundancy analyses, all indicated that penguins were responsible for the dissemination and high enrichment of ARGs in lake sediments via the guano deposition, which might greatly outweigh local human-activity effects. Our results revealed that ARGs could be carried into lakes across the Antarctica through penguin migration, food chains, and guano deposition, which were closely connected with the widespread pollution of ARGs at the global scale.

A seasonal study on the microbiomes of Diploid vs. Triploid eastern oysters and their denitrification potential

Oyster reefs are hotspots of denitrification mediated removal of dissolved nitrogen (N), however, information on their denitrifier microbiota is scarce. Furthermore, in oyster aquaculture, triploids are often preferred over diploids, yet again, microbiome differences between oyster ploidies are unknown. To address these knowledge gaps, farmed diploid and triploid oysters were collected over an annual growth cycle and analyzed using shotgun metagenomics and quantitative microbial elemental cycling (QMEC) techniques. Regardless of ploidy, Psychrobacter genus was abundant, with positive correlations found for genes of central metabolism, DNA metabolism, and carbohydrate metabolism. MAGs (metagenome-assembled genomes) yielded multiple Psychrobacter genomes harboring norB, narH, narI, and nirK denitrification genes, indicating their functional relevance within the eastern oysters. QMEC analysis indicated the predominance of carbon (C) and nitrogen (N) cycling genes, with no discernable patterns between ploidies. Among the N-cycling genes, the nosZII clade was overrepresented, suggesting its role in the eastern oyster's N removal processes.

Effects of Replacing Soybean Meal with Cottonseed Meal, Peanut Meal, Rapeseed Meal, or Distillers' Dried Grains with Solubles on the Growth Performance, Nutrient Digestibility, Serum Parameters, and Rumen Fermentation in Growing Lambs

Considering the frequently large price fluctuations for soybean meal, an alternative is the increased use of locally produced high-protein ingredients. The objective of this study was to evaluate the effects of the total replacement of soybean meal with different sources of protein on the growth performance, nutrient digestibility, serum parameters, rumen fermentation parameters, and bacterial communities in growing lambs. Sixty sheep with similar body weights (38.46 ± 0.71 kg) were distributed to one of five treatments: soybean meal (SBM); cottonseed meal (COM); peanut meal (PEM); rapeseed meal (RAM); and distillers' dried grains with solubles (DDGS). The experiment lasted 62 days with a 10-day adaptation period and a 52-day growing period. The results indicated that the body weight and average daily gain were not affected by different protein sources (p > 0.05), but the dry matter intake of the SBM group was lower than that of the other groups (p < 0.05); otherwise, the feed efficiency was higher (p < 0.05). The digestion of dry matter was higher in the SBM, COM, and RAM groups than in the DDGS and PEM groups (p < 0.05). Meanwhile, compared to the other groups, the SBM group had the highest digestion of gross energy and crude protein (p < 0.05). In addition, the concentration of glutathione peroxidase was highest in the SBM group (p < 0.05). Regarding the rumen fermentation, the SBM group had the highest concentration of NH3-N (p < 0.05). The rumen bacterial community was not affected by treatments (p > 0.05). In conclusion, the total replacement of soybean meal with cottonseed, peanut, rapeseed, or DDGS reduced digestibility but did not impact the body weight or average daily gain of growing lambs and had no effect on the immune function and rumen bacterial community; thus, they can be used to substitute the soybean meal.

Utilizing co-abundances of antimicrobial resistance genes to identify potential co-selection in the resistome

The rapid spread of antimicrobial resistance (AMR) is a threat to global health, and the nature of co-occurring antimicrobial resistance genes (ARGs) may cause collateral AMR effects once antimicrobial agents are used. Therefore, it is essential to identify which pairs of ARGs co-occur. Given the wealth of next-generation sequencing data available in public repositories, we have investigated the correlation between ARG abundances in a collection of 214,095 metagenomic data sets. Using more than 6.76∙108 read fragments aligned to acquired ARGs to infer pairwise correlation coefficients, we found that more ARGs correlated with each other in human and animal sampling origins than in soil and water environments. Furthermore, we argued that the correlations could serve as risk profiles of resistance co-occurring to critically important antimicrobials (CIAs). Using these profiles, we found evidence of several ARGs conferring resistance for CIAs being co-abundant, such as tetracycline ARGs correlating with most other forms of resistance. In conclusion, this study highlights the important ARG players indirectly involved in shaping the resistomes of various environments that can serve as monitoring targets in AMR surveillance programs.

IMPORTANCE

Understanding the collateral effects happening in a resistome can reveal previously unknown links between antimicrobial resistance genes (ARGs). Through the analysis of pairwise ARG abundances in 214K metagenomic samples, we observed that the co-abundance is highly dependent on the environmental context and argue that these correlations can be used to show the risk of co-selection occurring in different settings.

Chlorophyllin Supplementation of Medicated or Unmedicated Swine Diets Impact on Fecal Escherichia coli and Enterococci

Considering that certain catabolic products of anaerobic chlorophyll degradation inhibit efflux pump activity, this study was conducted to test if feeding pigs a water-soluble chlorophyllin product could affect the antibiotic resistance profiles of select wild-type populations of fecal bacteria. Trial 1 evaluated the effects of chlorophyllin supplementation (300 mg/meal) on fecal E. coli and enterococcal populations in pigs fed twice daily diets supplemented without or with ASP 250 (containing chlortetracycline, sulfamethazine and penicillin at 100, 100 and 50 g/ton, respectively). Trial 2, conducted similarly, evaluated chlorophyllin supplementation in pigs fed diets supplemented with or without 100 g tylosin/ton. Each trial lasted 12 days, and fecal samples were collected and selectively cultured at 4-day intervals to enumerate the total numbers of E. coli and enterococci as well as populations of these bacteria phenotypically capable of growing in the presence of the fed antibiotics. Performance results from both studies revealed no adverse effect (p > 0.05) of chlorophyllin, antibiotic or their combined supplementation on average daily feed intake or average daily gain, although the daily fed intake tended to be lower (p = 0.053) for pigs fed diets supplemented with tylosin than those fed diets without tylosin. The results from trial 1 showed that the ASP 250-medicated diets, whether without or with chlorophyllin supplementation, supported higher (p < 0.05) fecal E. coli populations than the non-medicated diets. Enterococcal populations, however, were lower, albeit marginally and not necessarily significantly, in feces from pigs fed the ASP 250-medicated diet than those fed the non-medicated diet. Results from trial 2 likewise revealed an increase (p < 0.05) in E. coli and, to a lesser extent, enterococcal populations in feces collected from pigs fed the tylosin-medicated diet compared with those fed the non-medicated diet. Evidence indicated that the E. coli and enterococcal populations in trial 1 were generally insensitive to penicillin or chlortetracycline, as there were no differences between populations recovered without or with antibiotic selection. Conversely, a treatment x day of treatment interaction observed in trial 2 (p < 0.05) provided evidence, albeit slight, of an enrichment of tylosin-insensitive enterococci in feces from the pigs fed the tylosin-medicated but not the non-medicated diet. Under the conditions of the present study, it is unlikely that chlorophyllin-derived efflux pump inhibitors potentially present in the chlorophyllin-fed pigs were able to enhance the efficacy of the available antibiotics. However, further research specifically designed to optimize chlorophyll administration could potentially lead to practical applications for the swine industry.

Occurrence and seasonal variations of antibiotic micro-pollutants in the Wei River, China

In this study, a systematic monitoring campaign of 30 antibiotics belonging to tetracyclines (TCs), macrolides (MLs), fluoroquinolones (FQs) and sulfonamides (SAs) was performed in the Xi'an section of the Wei River during three sampling events (December 2021, June 2022, and September 2022). The total concentrations of antibiotics in water ranged from 297 to 461 ng/L with high detection frequencies ranging from 45% to 100% for the various antibiotics. A marked seasonal variation in concentrations was found with total antibiotic concentrations in winter being 1.5 and 2 times higher than those in the summer and autumn seasons, respectively. The main contaminants in both winter and summer seasons were FQs, but in the autumn SAs were more abundant, suggesting different seasonal sources or more effective runoff for certain antibiotics during periods of rainfall. Combined analysis using redundancy and clustering analysis indicated that the distribution of antibiotics in the Wei River was affected by the confluence with dilution of tributaries and outlet of domestic sewage. Ecological risk assessment based on risk quotient (RQ) showed that most antibiotics in water samples posed insignificant risk to fish and green algae, as well as insignificant to low risk to Daphnia. The water-sediment distribution coefficients of SAs were higher than those of other antibiotics, indicating that particle-bound runoff could be a significant source for this class of antibiotics.

Non-Canonical Aspects of Antibiotics and Antibiotic Resistance

The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.

Insight into environmental adaptability of antibiotic resistome from surface water to deep sediments in anthropogenic lakes by metagenomics

The escalating antibiotic resistance threatens the long-term global health. Lake sediment is a vital hotpot in transmitting antibiotic resistance genes (ARGs); however, their vertical distribution pattern and driving mechanisms in sediment cores remain unclear. This study first utilized metagenomics to reveal how resistome is distributed from surface water to 45 cm sediments in four representative lakes, central China. Significant vertical variations in ARG profiles were observed (R2 = 0.421, p < 0.001), with significant reductions in numbers, abundance, and Shannon index from the surface water to deep sediment (all p-values < 0.05). ARGs also has interconnections within the vertical profile of the lakes: twelve ARGs persistently exist all sites and depths, and shared ARGs (e.g., vanS and mexF) were assembled by diverse hosts at varying depths. The 0-18 cm sediment had the highest mobility and health risk of ARGs, followed by the 18-45 cm sediment and water. The drivers of ARGs transformed along the profile of lakes: microbial communities and mobile genetic elements (MGEs) dominated in water, whereas environmental variables gradually become the primary through regulating microbial communities and MGEs with increasing sediment depth. Interestingly, the stochastic process governed ARG assembly, while the stochasticity diminished under the mediation of Chloroflexi, Candidatus Bathyarcaeota and oxidation-reduction potential with increasing depth. Overall, we formulated a conceptual framework to elucidate the vertical environmental adaptability of resistome in anthropogenic lakes. This study shed on the resistance risks and their environmental adaptability from sediment cores, which could reinforce the governance of public health issues.

External carbon source as a viable tool for controlling antibiotics and antibiotic resistance genes (ARGs) in effluent: Influence on antibiotic removal and ARGs dissemination

Fluoroquinolone antibiotics and antibiotic resistance genes (ARGs) regarded as emerging contaminants were poorly removed in conventional wastewater treatment plants (WWTPs). Nitrogen-containing heterocyclic organics were found to be biodegraded through denitrification co-metabolism. The feasibility to enhance antibiotics removal efficiency in WWTPs through denitrification co-metabolism needs to be further verified. Meanwhile, due to significant correlation between ARGs profiles and nitrogen removal that was previously observed, the dissemination of ARGs during denitrification was worthy of in-depth understanding. Herein, the antibiotic removal and ARGs dissemination in denitrification co-metabolism condition were investigated with different denitrifying consortiums that acclimated under different conditions in terms of carbon source and the exposure of Ofloxacin (OFL). The results suggest that the removal of OFL can be enhanced by the denitrification co-metabolism. The tolerance to OFL is different among various denitrifying communities. For the denitrifying consortiums acclimated with methanol, long-term exposure to trace OFL (1 μg/L) could reduce the capabilities of removal and tolerance to OFL. On the contrary, those acclimated with sodium acetate (NaAc), the capabilities of removal and tolerance to OFL, were enhanced by long-term exposure to trace OFL. According to the quantitative determination to 384 target genes with high-throughput quantitative PCR, the abundance of ARGs in consortiums greatly increased when exposed to OFL at the concentration of comparable to sewage, which was also much larger than that acclimated with methanol. It can be confirmed and supported by DNA sequencing results that the antibiotic removal and the dissemination of ARGs were determined by microbial community that could be shaped with carbon source. These conclusions suggest that selecting the right external carbon source can be a useful strategy for WWTPs to control antibiotics and ARGs in the effluent. From a new perspective on mitigating ARGs dissemination, NaAc was not an appropriate carbon source.

Contribution of pks+ Escherichia coli (E. coli) to Colon Carcinogenesis

Colorectal cancer (CRC) stands as a significant global health concern, ranking second in mortality and third in frequency among cancers worldwide. While only a small fraction of CRC cases can be attributed to inherited genetic mutations, the majority arise sporadically due to somatic mutations. Emerging evidence reveals gut microbiota dysbiosis to be a contributing factor, wherein polyketide synthase-positive Escherichia coli (pks+ E. coli) plays a pivotal role in CRC pathogenesis. pks+ bacteria produce colibactin, a genotoxic protein that causes deleterious effects on DNA within host colonocytes. In this review, we examine the role of the gut microbiota in colon carcinogenesis, elucidating how colibactin-producer bacteria induce DNA damage, promote genomic instability, disrupt the gut epithelial barrier, induce mucosal inflammation, modulate host immune responses, and influence cell cycle dynamics. Collectively, these actions foster a microenvironment conducive to tumor initiation and progression. Understanding the mechanisms underlying pks+ bacteria-mediated CRC development may pave the way for mass screening, early detection of tumors, and therapeutic strategies such as microbiota modulation, bacteria-targeted therapy, checkpoint inhibition of colibactin production and immunomodulatory pathways.

Progression of swine fecal microbiota during early stages of life and its association with performance: a longitudinal study

BACKGROUND

It is vital to understand healthy gut microbiota composition throughout early life stages when environments are changing, and immunity is developing. There are limited large-scale longitudinal studies classifying healthy succession of swine microbiota. The objectives of this study were to (a) determine the microbiota composition of fecal samples collected from piglets within a few days after birth until one-week post-weaning, and (b) investigate the associations of early fecal microbiota with pig growth performance in nursery and later growing stages. Fecal samples were collected from nine cohorts of 40 pigs (n = 360) from distinct farrowing sources in Ontario and Quebec, Canada at four timepoints from birth to one-week post-weaning, with pig body weight was recorded at each fecal sampling.

RESULTS

Microbiota was dominated by the phyla Firmicutes, Bacteroides and Proteobacteria. There were notable differences in genera abundance between pigs from different provinces and farming systems. Over the early life stage, the genera Bacteroides, Escherichia/Shigella, and Clostridium cluster XIVa were abundant preweaning, while Prevotella dominated post-weaning. Hierarchical clustering identified three major stages of microbiota development, each associated with distinct composition. Stage one occurs from birth to 7 days, stage two from 7 days after birth until weaning, and stage three from weaning to one-week post-weaning. Three enterotypes were identified in stage two that showed differences in growth before weaning, and in the grower production stage. Piglets with a microbiota enterotype characterized by higher abundance of Prevotella and unclassified Ruminococcaceae had lower growth performance in the pre-weaning stage, and the growing stage.

CONCLUSION

These findings help identify the timing of microbiota shifts across early swine life which may be the optimal time for external intervention to shift the microbiota to a beneficial state. The project findings should help decrease antimicrobial use, increase animal welfare, and have positive economic impacts.

Zoonotic bacteria in the vicinity of animal farms as a factor disturbing the human microbiome: a review

This review is aimed at summarizing the current state of knowledge about the relationship between environmental exposure to the bioaerosol emitted by intensive livestock farming and changes in the microbiome of people living in livestock farm vicinity. The PubMed, Scopus and Web of Science databases were searched by crossing keywords from the following 3 groups: a) "livestock," "animal farms," "animal breeding"; b) "microbiome," "resistome"; c) "livestock vicinity," "farm vicinity," "neighborhoods and health" in 2010-2022. Literature screening did not reveal any paper related to the full microbiome composition in the population studied. In the study, the authors included 7 papers (5 from the Netherlands, 1 from the USA, and 1 from China). The studies confirmed the carriage of Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), livestockassociated MRSA (LA-MRSA MC398) and multidrug-resistant S. aureus (MDRSA) in the nasal microbiome of adults and children living within 500-2000 m from a livestock farm. Clostridium difficile, including LA-ribotype RT078 carriage, was detected in the intestinal microbiome of adults living within 500-1000 m. Extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae were confirmed in the intestinal microbiome of adults living within 500-6200 m. Knowledge on the composition of the microflora of people living in livestock farm vicinity is insufficient to conclude about changes in the microbiome caused by the environmental emission of bioaerosol. The carriage prevalence of the LA-bacteria, including both strains with antimicrobial resistance and antimicrobial resistance genes, confirms the presence of zoonotic bacteria in the human microflora in populations without occupational contact with animals. It cannot be ruled out that zoonotic bacteria, as a component of the microbiome, have a negative impact on people's health. Int J Occup Med Environ Health. 2024;37(2):138-52.