Microbial Profiles Research Articles

Analyses of the gut microbial composition of domestic pig louse Haematopinus suis

Haematopinus suis is an obligatory ectoparasite of the domestic pig, serving as a vector of several swine pathogens and posing great threats to the pig industry. The gut microbiome of lice is thought of an important mediator of their healthy physiology. However, there is a great paucity of lice-associated microbial communities’ structure and function. The current study aimed to profile the gut microbiome and to understand the microbial functions of swine lice by metagenomic sequencing and bioinformatics analyses. In total, 102,358 (77.2 %) nonredundant genes were cataloged, by contrast, only a small proportion of genes were assigned to microbial taxa and functional assemblages. Bacteria of known or potential public health significance such as Anaplasma phagocytophilum, Chlamydia trachomatis, Waddlia chondrophila, Bacillus cereus, and Leptotrichia goodfellowii were observed in all samples. The integrated microbial profile further illustrated the evolutionary relevance of endosymbionts and detailed the functional composition, and findings suggested H. suis may acquire adenosylcobalamin by feeding due to an adenosylcobalamin synthesis defect and a lack of complete synthases of endosymbionts. Sucking lice contained fewer functional genes compared with ticks and fleas probably because of the obligate host specificity of parasitic lice. In addition, the genes from the intestines contained encompassed most of the microbial functional genes in sucking lice. A wide range of unknown taxonomic and functional assemblages were discovered, which improves our understanding related to microbial features and physiological activities of sucking lice. In general, this study increases the characterization of the microbiota of lice and offers clues for preventing and controlling lice infestation in swine production in the future.

Influence of Drugs and Toxins on Decomposition Dynamics: Forensic Implications

Drug and toxin-related deaths are common worldwide, making it essential to detect the postmortem concentration of various toxic substances at different stages of decomposition in a corpse. Indeed, determining the postmortem interval (PMI) and cause of death in an advanced stage of decomposed corpses has been a significant challenge in forensic investigations. Notably, the presence of drugs or toxins can have a significant impact on the microbial profile, potentially altering the succession of microbial communities and subsequent production of volatile organic compounds (VOCs), which, in turn, affect insect colonization patterns. This review aims to highlight the importance of investigating the interactions between drugs or toxins, microbial succession, VOC profiles, and insect behavior, which can provide valuable insights into forensic investigations as well as the ecological consequences of toxins occurring in decomposition. Overall, the detection of drugs and other toxins at different stages of decomposition can yield more precise forensic evidence, thereby enhancing the accuracy of PMI estimation and determination of the cause of death in decomposed remains.

Comparative Ecotoxicity Assessment of highly bioactive Isomeric monoterpenes carvacrol and thymol on aquatic and edaphic indicators and communities

The growing demand for sustainable natural products to replace harmful synthetic ones requires comprehensive ecotoxicity assessments to ensure their eco-friendly nature. This study explored for the first time the changes in microbial community growth and metabolic profiles from river and natural soil samples exposed to the two structural isomers, thymol (THY) and carvacrol (CARV), utilizing Biolog EcoPlate™ assays and 16S rRNA gene sequencing for taxonomic analysis. In addition, we addressed existing ecotoxicity data gaps for these two compounds by using aquatic (Daphnia magna and Vibrio fischeri) and soil (Eisenia fetida and Allium cepa) indicators. Results show acute toxicity of both CARV and THY on all indicators. V. fischeri (LC50=0.59 mg/L) >D. magna (4.75 mg/L) >A. cepa (6.47 mg/L) for CARV, and V. fischeri (LC50=1.71 mg/L) >A. cepa (4.05 mg/L) >D. magna (8.13 mg/L) for THY. E. fetida showed LC50 = 7.68 mg/Kg for THY and 1.04 for CARV. River and soil microbial communities showed resilience, likely because they contain taxa capable of biodegrading these products. No significant growth inhibition effects were observed up to 100 mg/L, though substrate utilization decreased at higher concentrations, particularly for polymers and amines in soil microorganisms and polymers in aquatic communities. Soil microorganisms were more affected than aquatic ones, with CARV being more toxic than THY (EC50120h = THY 94.13 and CARV 29.79 mg/L in soil microorganisms). These findings suggest that an increase in the consumption of these products and their subsequent ecotoxicity effects from environmental discharge should still be monitored before being ruled out. However, long-term effects are unlikely due to microbial degradation of these natural products, potentially reducing risks to other target species and opening the way for their use as substitutes for commercial antibiotics.

Impact of COVID-19 on the Prevalence and Drug Resistance of Bacteria Isolated From Bacterial Meningitis Cerebrospinal Fluid in Shandong Province: A Multicenter Retrospective Study.

Our objective was to evaluate the ramifications of the 2019 coronavirus disease (COVID-19) pandemic on the microbial profile and antimicrobial resistance patterns of bacteria isolated from cerebrospinal fluid (CSF) specimens of patients with bacterial meningitis. We conducted a retrospective analysis of laboratory results and clinical records about positive CSF cultures reported by the SPARSS network from 2017 to 2023. The study covered three distinct periods: January 2017 to December 2019 (before the COVID-19 pandemic), January 2020 to December 2022 (during the COVID-19 pandemic), and January 2023 to December 2023 (after the COVID-19 pandemic), with a total of 5793 CSF isolates collected. Notably, the proportion of male patients (61.3%) was higher than that of females. After COVID-19, we observed a notable shift in the seasonal peak of CSF pathogens, with a delay of approximately 3 months. Remarkable alterations were evident in both pediatric and adult CSF isolate profiles. In children, the predominant pathogens included coagulase-negative Staphylococcus (CoNS), Streptococcus pneumonia, and Escherichia coli. Notably. After COVID-19, there was a significant decrease in the proportion of CoNS (p = 0.0039) and a notable increase in E. coli (p = 0.0067). In adults, the top three pathogens were CoNS, Acinetobacter baumannii, and Klebsiella pneumoniae. After the pandemic, we observed a significant reduction in the prevalence of A. baumannii (p = 0.0059), while the proportions of K. pneumoniae, Pseudomonas aeruginosa, Enterobacter cloacae, and Enterococcus faecalis increased significantly (p < 0.05). Additionally, among multidrug-resistant bacteria, the detection rate of carbapenem-resistant E. coli escalated (p = 0.0375). Antimicrobial susceptibility analysis indicated a declining trend in resistance rates for CoNS and A. baumannii to certain antibiotics following the pandemic. Conversely, resistance to imipenem in A. baumannii increased. In conclusion, the COVID-19 pandemic has significantly influenced the composition, antimicrobial resistance patterns, and epidemiological dynamics of CSF-isolated bacteria in Shandong province. To effectively address these changes, ongoing and dynamic surveillance of pathogen trends and antimicrobial resistance rate is essential.

Characterization of psychrotrophic and thermoduric bacteria in raw milk using a multi-omics approach.

Psychrotrophic and thermoduric bacteria are the main reasons for the spoilage of dairy products. This study aims to address the composition and function of psychrotrophic and thermoduric bacteria in eight groups of raw milk samples obtained from Heilongjiang Province and Inner Mongolia (China). Microbial enumeration showed an average total bacterial count of 4.63 log c.f.u. ml-1 and psychrotrophic bacterial counts of 4.82 log c.f.u. ml-1. The mean counts of mesophilic and thermophilic thermoduric bacteria were 3.68 log and 1.81 log c.f.u. ml-1, respectively. Isolated psychrotrophic bacteria (26 genera and 50 species) and mesophilic thermoduric bacteria (20 genera and 32 species) showed high microbial diversity. Through metagenomic and proteomic analyses, significant disparities in the concentration and community structure of psychrotrophic and thermoduric bacteria were observed among different locations. A large number of peptidases were annotated by metagenomics, which may result in milk spoilage. They mainly come from some typical psychrotrophic and thermoduric bacteria, such as Chryseobacterium, Epilithonimonas, Pseudomonas, Psychrobacter, Acinetobacter, Lactococcus, Escherichia and Bacillus. However, the main proteins detected in fresh raw milk were associated with bacterial growth, reproduction and adaptation to cold environments. This investigation provides valuable insights into the microbial communities and protein profiles of raw milk, shedding light on the microbial factors contributing to milk deterioration.

Strategic alteration of arabinoxylan feruloylation enables selective shaping of the human gut microbiota

Arabinoxylans (AXs) are promising prebiotic candidates abundant in cereals. While AX feruloylation impacts properties, its effects on long chains mimicking native structures are unclear. This study revealed a dose-dependent impact of long chain AX feruloylation on gut microbial composition and function. In vitro fecal fermentation with varying AX feruloylation showed increased Bacteroidetes and propionate along with decreased Firmicutes and butyrate. Distinct Bacteroides populations were enriched under different feruloylation levels, suggesting specialized adaptation. Community dynamics and co-occurrence networks highlighted intricate taxon-specific responses, underscoring the unique microbial profiles shaped by individual variations. This study lays the foundation for elucidating the metabolic pathways and enzymatic machineries enabling utilization of feruloylated AXs based on the dose-dependent enrichment of specific taxa. This knowledge can inform rational design of customized prebiotics through precision nutrition. This work provides novel insights into tailoring cereal biomass fermentation and microbiome structure-function relationships. It establishes a platform for developing optimized feruloylated prebiotics to deliberately modulate gut ecology and address intestinal dysbiosis.

Microbial profile of burn wound injuries in the Northern West Bank − A retrospective cohort study

BackgroundDetermining frequently colonizing microorganisms and typical demographics affected by burns in the West Bank is essential to aid timely and effective injury management. MethodsThis study included n = 435 patients with burn injuries between January 2018-December 2021 at a tertiary center in Nablus. Eligible medical records were reviewed, and relevant data extracted. Resultsn = 244 males and n = 191 females, average age 14.5 years were included. n = 227 had wound swab cultures, n = 80 which were positive. Scald injuries were the most common mechanism of injury (n = 314, n = 162 in males (p < 0.001), average age of 10.5 years). The most common organisms isolated were Pseudomonas aeruginosa (n = 17) and Staphylococcus aureus (n = 18). n = 17 multidrug resistant (MDR) organisms were cultured, MRSA most commonly (n = 9), followed by K. pneumoniae (ESBL) (n = 5). Overall length of stay (LOS) was 17.27 days in all patients and 28.2 days in those with MDR, with increasing LOS significantly associated with positive culture and MDR development of MDR (p < 0.001). ConclusionsYounger male demographics and longer hospital admission increase the risk of burn wound colonization and MDR development in the Northern West Bank. Pseudomonas aeruginosa and Staphylococcus aureus were prevalent organisms isolated. MDR development represents a significant challenge in the effective management of injuries in an immunologically vulnerable cohort.

Comparison of the aetiology, microbiological isolates and antibiotic susceptibilities of endophthalmitis between children and adults in southern China: a retrospective, cohort study

ObjectivesTo compare aetiology, microbiological isolates and antibiotic susceptibilities of endophthalmitis between children and adults.DesignRetrospective observational study.ParticipantsPatients admitted to Zhongshan Ophthalmic Center between January 2013 and December 2019 with clinically diagnosed...

Imprints of Soil Microbial Activity Accredited to Residue-Management and Tillage Practices for Boosting Rice and Wheat Production

The sustainable productivity of rice–wheat cropping systems relies on soil health, and soil health can be positively influenced by treating previous crop residues using conservation tillage practices. The present study examined the impact of three rice residue-management practices under zero-tilled wheat (ZTW) and conventionally tilled wheat (CTW), along with two rice-sowing practices, during rice cultivation on soil functional microbial diversity, physiological profiling, and grain yields of rice and wheat. Anchored residues (ARs) under ZTW exhibited significantly (p ≤ 0.05) high average well color development—31.43% more than CTW with no residue (NR). CTW with residue burning (BUR) showed a 5.42% increase in the Shannon diversity index compared to CTW-NR. Substrate richness was 10.02% higher in CTW-BUR compared to CTW-NR. CTW-BUR demonstrated the highest 17.98% increase in the Shannon evenness index compared to CTW-NR. The direct-seeded rice (DSR) system generally surpassed puddled transplanted rice (PTR) in most indices, except for the Shannon evenness index values. ZTW-AR exhibited the highest utilization of amino acids, carboxylic acids, and phenolic compounds, while CTW-BUR exhibited the highest utilization of carbohydrates and polymers utilization, and ZTW with no-residue (NR) exhibited the highest utilization of amines. Rice and wheat grain yields were highest with full residue in ZTW and lowest in CTW-NR. PTR supported higher rice yields, while DSR was superior for wheat. These findings highlight the favorable role of residue retention with no tillage during wheat cultivation in the maintenance of soil quality and rice–wheat productivity.

Predicting the Microbiome and Metabolome Dynamics of Natural Apple Fermentation Towards the Development of Enhanced Functional Vinegar

Natural vinegar fermentation is a complex process influenced by the interplay between microbial communities and metabolites. This study examined the interplay between the microbiome and the metabolome over a three-month period, with samples collected every ten days. Using Illumina sequencing and chromatographic techniques (HPLC and GC-MS), we mapped microbial shifts and metabolite profiles. Early fermentation showed a diverse microbial presence, including genera such as Cronobacter, Luteibacter, and Saccharomyces. A stable microbial ecosystem established between days 15 and 70, characterized by the dominance of Leuconostoc, Gluconobacter, and Saccharomyces, which facilitated consistent substrate consumption and metabolite production, including various organic acids and ethanol. By day 70, Acetobacter prevalence increased significantly, correlating with a peak acetic acid production of 12.4 g/L. Correlation analyses revealed significant relationships between specific microbes and volatile organic compounds. This study highlights the crucial roles of these microbes in developing sensory profiles suited for industrial applications and proposes an optimal microbial consortium for enhancing vinegar quality. These data suggest that an optimal microbial consortium for vinegar fermentation should include Saccharomyces for efficient alcohol production, Leuconostoc for ester-mediated flavor complexity, and Acetobacter for robust acetic acid production. The presence of Komagataeibacter could further improve the sensory and functional qualities due to its role in producing bacterial cellulose.

Whole-Genome Metagenomic Analysis of Functional Profiles in the Fecal Microbiome of Farmed Sows with Different Reproductive Performances

Recent studies suggested an association between the reproductive performance of sows and their gut microbiota. To understand how the gut microbiota affect the reproductive performances of sows, we conducted a whole-genome metagenomic analysis on the fecal microbial functional profiles of sows with high and low reproductive performances. We used 60 sows from six farms (10 sows/farm), including 30 sows from three farms with higher reproductive performances (the mean number of weaned piglets/sow/year) (group H) and 30 sows from three farms with lower performances (group L). Fecal microbial DNA was subjected to a whole-genome metagenomic analysis. Biomarker exploration analysis identified “carbohydrate transport and metabolism” as the most discriminative function enriched in group H. Further analysis of carbohydrate-active enzymes revealed that the fecal microbiome of group H had a greater capacity to degrade dietary fiber, specifically cellulose and pectin. Group H also exhibited higher fecal short-chain fatty acid (SCFA) concentrations than group L, with the abundances of cellulose- and pectin-degrading genes showing significant positive correlations with fecal SCFA concentrations. Taxonomic analysis indicated greater contributions of Prevotella, Treponema, Ruminococcus, and Fibrobacter to cellulose and pectin degradation in the fecal microbiome in group H. In conclusion, higher reproductive performances of sows were, at least in part, associated with a greater microbial capacity for degrading cellulose and pectin, resulting in a higher SCFA production in the hindgut.

Integrated multi-omics analysis of the microbial profile characteristics associated with pulmonary arterial hypertension in congenital heart disease.

Dysregulation of immune and inflammatory cells around blood vessels and metabolic dysfunction are key mechanisms in the development of pulmonary arterial hypertension (PAH). The homeostasis of the human microbiome plays a crucial role in regulating immune responses and the progression of diseases. For pulmonary arterial hypertension associated with congenital heart disease involving body-lung shunt (PAH-CHD), the potential impact of the microbiome on the "gut-lung axis" remains underexplored. This study recruited 15 healthy individuals and 15 patients with pulmonary arterial hypertension due to congenital heart disease from Fuwai Yunnan Hospital, Chinese Academy of Medical Sciences, and Kunming Children's Hospital. We performed differential analyses of metabolites and microbiota from both the gut and lower respiratory tract for these two groups. The goal was to investigate the "gut-lung axis" microbiome and metabolome profiles in children with PAH-CHD and to analyze the interrelationships between these profiles. Ultimately, we aim to propose the potential value of these profiles in aiding diagnosis. The results indicated that the gut and pulmonary microbiota of children with PAH-CHD are characterized by an increased abundance of beneficial symbionts, which are closely linked to changes in the metabolome. Metabolite functional enrichment analysis revealed energy metabolism reprogramming in the PAH-CHD group, with active metabolic pathways associated with bile acid secretion and carnitine homeostasis. Moreover, the differential expression of metabolites was correlated with right heart function and growth development.IMPORTANCEPrevious studies have primarily focused on the relationship between the gut microbiome and PAH. However, the impact of microbial homeostasis on the progression of PAH-CHD from the perspective of the gut-lung axis has not been adequately elucidated. Our study utilizes an integrated multi-omics approach to report on the differential characteristics of gut and lung microbiota between children with PAH-CHD and reference subjects. We found that microbiota influence the pathological changes and disease manifestations of PAH-CHD through their metabolic activity. Additionally, alterations in metabolites impact the microbial ecological structure. Our findings suggest that modulating the microbiome composition may have positive implications for maintaining and regulating the immune environment and pathological progression of PAH-CHD.

Exploring microbial diversity in Kermanshah province’s Kermanshahi oil through DGGE and sequencing analysis

BackgroundGhee, known as “roghane heiwâni,” or “Kermanshahi oil” is a traditional fermented butter-like product highly esteemed for its nutritional value. Ghee is prepared using traditional methods and has substantial potential as a reservoir of probiotic microorganisms. Previous research delved into isolating and identifying lactic acid bacteria (LAB) in Kermanshahi through culture and PCR sequencing. This study seeks to elucidate the microbial profiles and diversity within Kermanshahi using culture, Denaturing Gradient Gel Electrophoresis (DGGE), and sequencing methodologies.MethodsTwenty samples of Kermanshahi oil were meticulously gathered from diverse locales across Kermanshah province. These samples were cultivated under specialized conditions in MRS and M17 environments spanning 24 to 72 h. Following DNA extraction, amplification of the 16SrRNA gene sequences was performed, culminating in sequencing for conclusive identification of the isolates. Furthermore, the DGGE technique was directly employed to separate and identify various species present in the oil samples utilizing bioinformatics software.ResultsSequencing outcomes revealed a diverse array of microorganisms among the isolates, with Lactobacillus constituting 43%, Streptococcus comprising 27.6%, Enterococcus at 4.61%, and yeasts at 7.6%. Other species exhibited lower frequencies, encompassing Rhizobium, Bacillus coagulans, and Staphylococcus hominis.ConclusionsThe isolation of a diverse spectrum of probiotic microorganisms underscores their potential utility in the realm of industrial dairy product production. These findings allude to the possibility of integrating these valuable microorganisms, which have historically been associated with traditional products, into the contemporary dairy industry. As consumer interest in probiotic-enriched products surges, the insights gained from this study pave the way for harnessing the benefits of Kermanshahi-derived probiotics.

Investigation of Staphylococcus Spp and Coliform Bacteria Contamination Sources after Cleaning-in-Place in Production Lines of Dairy Factories in Türkiye.

Microorganisms detected on dairy factory surfaces after disinfection can cause product contamination, leading to economic losses and health hazards for consumers. In this study, the presence of Staphylococcus spp. and Coliform in a total of 450 samples taken from food-contact and non-contact surfaces (stainless steel, plastic, cloth, and tiles surfaces), raw milk and final product (white cheese, kashar cheese, butter, yogurt, and cream) samples in five dairy factories was investigated by conventional techniques. The isolates obtained were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry. In this study, a total of 54 Staphylococci (16.7% S. aureus and 81.5% coagulase-negative Staphylococci [CNS]) and 44 coliform isolates were identified at the species level. The most common CNS isolated by samples was S. epidermidis followed by S. saprophyticus, S. capitis, S. succinus S. carnosus. S. xylosus, S. sciuri, S. equorum, S. warneri, and S. hominis. Eighteen of the coliform isolates (41%) were identified as E. coli; 13 (29.5%) as E. cloacae; 3 (6.9%) as E. kobei, C. freundii, and K. oxytoca; 2 (4.5%) as K. pneumoniae; 1 (2.3%) as E. ludwigii and C. farmeri. The contamination rate of non-food contact surfaces (71.3%) was found to be higher than food contact surfaces (10.4%), and contaminated surfaces were found to be effective in product contamination. Study results show that some bacterial species obtained from raw milk, surfaces, and final products are factory specific and surface-associated bacteria are prominent in the product microbial profile.

Changes in Gut Microbial Composition and DNA Methylation in Obese Patients with NAFLD After Bariatric Surgery.

This study investigates the effects of bariatric surgery on non-alcoholic fatty liver disease (NAFLD) by examining the interplay between gut microbiota, epigenetics, and metabolic health. A cohort of 22 patients undergoing sleeve gastrectomy (SG) was analyzed for changes in gut microbial composition and DNA methylation profiles before and six months after surgery. Correlations between gut microbial abundance and clinical markers at baseline revealed that certain genera were associated with worse metabolic health and liver markers. Following SG, significant improvements were observed in the clinical, anthropometric, and biochemical parameters of the NAFLD patients. Although alpha-diversity indices (i.e., Chao1, Simpson, Shannon) did not show significant changes, beta-diversity analysis revealed a slight shift in microbial composition (PERMANOVA, p = 0.036). Differential abundance analysis identified significant changes in specific bacterial taxa, including an increase in beneficial Lactobacillus species such as Lactobacillus crispatus and Lactobacillus iners and a decrease in harmful taxa like Erysipelotrichia. Additionally, DNA methylation analysis revealed 609 significant differentially methylated CpG sites between the baseline values and six months post-surgery, with notable enrichment in genes related to the autophagy pathway, such as IRS4 and ATG4B. The results highlight the individualized responses to bariatric surgery and underscore the potential for personalized treatment strategies. In conclusion, integrating gut microbiota and epigenetic factors into NAFLD management could enhance treatment outcomes, suggesting that future research should explore microbiome-targeted therapies and long-term follow-ups on liver health post-surgery.

Living without pain: A 10-year study of congenital insensitivity to pain with anhidrosis.

Congenital Insensitivity to Pain with Anhidrosis (CIPA) is a rare hereditary neuropathy caused by NTRK1 gene mutations, predisposing patients to recurrent infections and chronic wounds. Long-term studies on microbial and clinical outcomes in CIPA are limited. This study presents analysis of infection patterns, antibiotic resistance, and clinical outcomes in CIPA patients. A comprehensive ten-year retrospective cohort study was conducted at Soroka University Medical Center, Beer Sheva, Israel, from January 2014 to January 2023. Electronic medical records were reviewed to identify 63 CIPA patients, all were of consanguineous Bedouin families. Data collection included demographic details, clinical presentations, genetic analysis, documentation of infections, wound sites, hospital duration, and surgical interventions. Staphylococcus aureus, notably methicillin-resistant, dominated, with Gram-negative bacteria common in lower limbs. The study noted reduced extended-spectrum beta-lactamase bacteria and linked demographic factors to infection traits, antibiotic resistance, and surgical needs. This study provides valuable insights into the clinical and microbial patterns of CIPA, highlighting dynamic shifts in microbial compositions and antibiotic resistance profiles over time. Staphylococcus aureus, and Gram-negative bacteria particularly in lower limb infections, pose significant challenges in patient management. The findings underscore the importance of tailored approaches to address evolving microbial profiles and optimize patient care in CIPA. Key Message: This is the largest cohort study on CIPA to date, highlighting the dominance of Staphylococcus aureus, including methicillin-resistant strains, and significant Gram-negative bacterial infections in lower limbs. Contribution to Literature: It draws parallels between infection dynamics in CIPA and diabetic foot ulcers, emphasizing similar challenges due to neuropathy and ischemia, enhancing understanding of infection susceptibility and management in neuropathic conditions. The findings inform clinical practices by detailing infection and resistance patterns, supporting the development of targeted treatment strategies to improve outcomes for CIPA and similar conditions.

Programming rumen microbiome development in calves with the anti-methanogenic compound 3-NOP

The aim of this study was to establish a distinctive rumen microbial and fermentation profile using the anti-methanogenic compound 3-NOP to assess dam effect, and nutritional intervention of the juvenile offspring on microbial structure and function of rumen up to 12 months of age, once the treatment was withdrawn. Forty-eight pregnant heifers (H) and their future offspring (C) were allocated to either Control (-) or 3-NOP (+) treatment resulting in four experimental groups: H+/C+, H+/C-, H-/C + and H-/C-. Animals were treated from 6 weeks prior to calving until weaning, with the offspring monitored until 12 months of age. Rumen fluid samples and methane measurements using the Greenfeed system were collected during the trial. Results supported the mode of action of the compound, with a shift in fermentation from acetate to propionate, increases in branched chain fatty acids and formic acid in the 3-NOP treated animals. Similar shifts in microbial populations occurred in 3-NOP treated animals with lower abundances of rumen methanogen populations, increases of bacterial groups Succiniclasticum spp, Candidatus Saccharimonas. Fibrobacter and the families Prevotellaceae and Succinivibrioacea. and the protozoa Entodinium. Early life intervention had an enduring impact on the rumen microbial structure of young animals up to 28 weeks post weaning, however the effect was diminished once 3-NOP was withdrawn. Interestingly, a group of young animals emitted significantly less methane (15%) than the animals that did not receive the treatment during their juvenile stage. Our results suggest a higher resemblance of the young calf microbiome to a low methane adult and that early life colonisation of the rumen persists through to later life with the pre-weaning microbiome comprising ~ 65% of the yearling animal. Further research needs to be performed to determine the timing and dose of 3-NOP for new-born calves that can sustain a reduction in methane emissions after the treatment is withdrawn, under extensive grazing or controlled conditions.

Microbial Dynamics and Pathogen Control During Fermentation of Distiller Grains: Effects of Fermentation Time on Feed Safety.

Determining the effects of fermentation duration on the microbial ecosystem, potential pathogenic risks, and metabolite generation during the fermentation of distilled grains is essential for safeguarding the safety and enhancing the nutritional profile of animal feed. This study investigates the effect of varying fermentation times (9, 30, and 60 days) on microbial diversity, pathogenic risk, and metabolite profiles in distiller grains using 16S rDNA sequencing and LC-MS-based metabolomics. The results showed that early fermentation (9-30 days) enhanced the abundance of beneficial bacteria, such as Lactobacillus reuteri and Lactobacillus pontis (p < 0.05), while pathogenic bacteria, like Serratia marcescens and Citrobacter freundii, were significantly reduced (p < 0.05). Metabolomic analysis revealed an increase in unsaturated fatty acids and the degradation of biogenic amines during early fermentation. However, prolonged fermentation (60 days) led to a resurgence of pathogenic bacteria and reduced the synthesis of essential metabolites. These findings suggest that fermentation duration must be optimized to balance microbial safety and nutrient quality, with 30 days being the optimal period to reduce pathogenic risks and enhance feed quality.

Effects of Formaldehyde-Treated Feed on Rumen Metabolism and Blood Biochemistry in Lambs: A Review

This review evaluates the impact of formaldehyde treatment on feed for lambs, focusing on its effects on rumen metabolism and blood biochemical indicators. Formaldehyde is commonly used as a feed additive to improve nutritional efficiency and preserve feed quality. This review synthesizes data from various studies to assess how formaldehyde-treated feed influences rumen fermentation parameters, including volatile fatty acid (VFA) production, rumen pH, and microbial activity. Additionally, the review examines the effects of formaldehyde treatment on key blood biochemical markers such as glucose, urea nitrogen, and liver enzymes. Studies indicate that formaldehyde treatment can enhance the stability and digestibility of feed, potentially improving nutrient utilization and overall animal performance. The preservation of protein and reduction in feed spoilage are highlighted as significant benefits, contributing to more consistent rumen function and metabolic efficiency. However, the impact on rumen microbial populations and VFA profiles shows mixed results, with some studies reporting improved microbial efficiency and others noting minimal changes. The review also discusses potential adverse effects, including alterations in blood biochemical parameters. While formaldehyde treatment generally maintains or improves key indicators like blood glucose and protein levels, excessive use may lead to concerns such as elevated urea nitrogen levels and potential liver enzyme disruptions, the review concludes that formaldehyde-treated feed can be a valuable tool in optimizing feed efficiency and lamb health, provided it is used judiciously. Future research is recommended to further elucidate the long-term effects on rumen microbiota and metabolic processes, ensuring balanced benefits without compromising animal welfare.

Assessing the pig microbial health impacts of smallholder farming

The livestock industry has long been a hotspot environment for antibiotic resistance genes, with smallholder farming still holding a significant position in pig farming. However, the microbial antibiotic resistance and pathogen risks in pigs under the smallholder farming model remain unclear. We systematically analyzed the antibiotic resistance and microbial composition of pig feces from smallholder and large-scale farming models in Sichuan. The results indicated a lower abundance of antibiotic resistance genes (ARGs) and similar microbial composition in smallholder farming compared to large-scale farming. Beneficial bacteria were more abundant in small-scale farming, whereas large-scale farming exhibited more ARGs, virulence genes, and human pathogenic bacteria (HPBs), including ESBL Escherichia coli strains closely related to human strains, indicating higher zoonotic risk. The findings suggest that smallholder farming presents a relatively better microbial composition and resistance profile, highlighting its advantages over large-scale farming in terms of pig and human health. It is noteworthy that a considerable proportion of HPBs carrying ARGs still exist in the feces from smallholder farming, and given the openness of fecal handling, there remains a high risk of transmitting ARGs and pathogens to humans.