Evaluation of DNA extraction methods of rumen microbial populations

The dynamism of microbial populations in the rumen has been studied with molecular methods that analyze single nucleotide polymorphisms of ribosomal RNA gene fragments (rDNA). Therefore DNA of good quality is needed for this kind of analysis. In this work we report the evaluation of four DNA extraction protocols (mechanical lysis or chemical lysis with CTAB, ethylxanthogenate or DNAzol^®) from ruminal fluid. The suitability of two of these protocols (mechanical lysis and DNAzol^®) was tested on single-strand conformation polymorphism (SSCP) of rDNA of rumen microbial populations. DNAzol^® was a simple method that rendered good integrity, yield and purity. With this method, subtle changes in protozoan populations were detected in young bulls fed with slightly different formulations of a supplement of multinutritional blocks of molasses and urea. Sequences related to Eudiplodinium maggi and a non-cultured Entodiniomorphid similar to Entodinium caudatum, were related to major fluctuating populations in an SSCP assay.     

Effects of different sources of physically effective fiber on rumen microbial populations

Physically effective fiber is needed by dairy cattle to prevent ruminal acidosis. This study aimed to examine the effects of different sources of physically effective fiber on the populations of fibrolytic bacteria and methanogens. Five ruminally cannulated Holstein cows were each fed five diets differing in physically effective fiber sources over 15 weeks (21 days/period) in a Latin Square design: (1) 44.1% corn silage, (2) 34.0% corn silage plus 11.5% alfalfa hay, (3) 34.0% corn silage plus 5.1% wheat straw, (4) 36.1% corn silage plus 10.1% wheat straw, and (5) 34.0% corn silage plus 5.5% corn stover. The impact of the physically effective fiber sources on total bacteria and archaea were examined using denaturing gradient gel electrophoresis. Specific real-time PCR assays were used to quantify total bacteria, total archaea, the genus Butyrivibrio, Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens and three uncultured rumen bacteria that were identified from adhering ruminal fractions in a previous study. No significant differences were observed among the different sources of physical effective fiber with respect to the microbial populations quantified. Any of the physically effective fiber sources may be fed to dairy cattle without negative impact on the ruminal microbial community.     

Inhibitory effects of phytochemicals on NLRP3 inflammasome activation: A review

BackgroundThe NLRP3 inflammasome formation and following cytokine secretion is a crucial step in innate immune responses. Internal and external factors may trigger inflammasome activation and result in inflammatory cytokine secretion. Inflammasome formation and activity play critical roles in several disease pathologies such as cardiovascular, metabolic, renal, digestive, and CNS diseases. Underlying pathways are not yet clear, but phytochemicals as alternative therapies have been extensively used for suppression of inflammatory responses.PurposeIn this review, we aimed to summarize in vivo and in vitro effects on NLRP3 inflammasome activation of selected phytochemicals.MethodThree phytochemicals; Sulforaphane, Curcumin, and Resveratrol were selected, and studies were reviewed to clarify their intracellular signaling mechanism in NLRP3 inflammasome activity. PubMed and Scopus databases are used for the search. For sulforaphane, 8 articles, for curcumin, 25 articles, and for resveratrol, 41 articles were included in the review.ConclusionIn vitro and in vivo studies pointed out that the selected phytochemicals have inhibitory properties on NLRP3 inflammasome activity. However, neither the mechanism is clear, nor the study designs and doses are standardized.     

Studies on the effects of selenium on rumen microbial fermentation in vitro

The effects of selenium (Se) on ruminant microbial fermentation were investigated in vitro using rumen microflora collected from a rumen-fistulated dairy cow. First, the effects ofl-selenomethionine (SeMet; at 0.2 or 2 ppm Se) in the presence or absence of wheat bran (WB, 500 mg per incubation flask) were evaluated. Second, the effects of several forms of Se (elemental Se: 50 ppm Se; sodium selenite: 2 ppm Se; SeMet: 2 ppm Se) were compared. Results showed that the amounts of short-chain fatty acids (SCFAs) tended to be increased by SeMet treatment, whereas SeMet in the presence of WB transiently suppressed fermentation. The addition of SeMet tended to increase the production of acetate while reducing the production of butyrate with and without WB supplementation. Among the different Se compounds tested, the amounts of SCFAs were greater with SeMet treatment, which yielded a higher proportion of acetate compared to other treatments. Selenite did not influence the total SCFAs concentrations; however, it increased the relative proportion of butyrate at the expense of acetate. Elemental Se did not significantly affect fermentation. Higher bacterial Se concentrations were observed for selenite than for SeMet. It was concluded that Se supplementation can influence rumen microbial fermentation and that Se compounds differ in this regard.     

Influence of phytochemicals on the biocompatibility of inorganic nanoparticles: a state-of-the-art review

Inorganic nanoparticles (NPs) are among the most produced NPs that could be used in consumer products and as healthcare materials, however, the intrinsic toxicity particularly through the mechanism associated oxidative stress raises the health concern about inorganic NP exposure. Phytochemicals are bioactive metabolites derived from plants as well as non-pathogenic microorganisms living within plants and have been shown to be beneficial to human health with their anti-aging, anti-cancer, anti-inflammation and anti-oxidant properties. In the present review, the influence of on the biocompatibility of inorganic NPs was discussed. It has been shown that phytochemicals could be used as bio-friendly capping agents for green synthesis of inorganic NPs, and phytochemical coated inorganic NPs were remarkable stable and biocompatible with high therapeutic efficiency. Meanwhile, the presence of phytochemicals was also able to reduce the side effects and enhance the therapeutic abilities of inorganic NPs, which is likely attributed to the anti-oxidative properties of phytochemicals. Thus, using phytochemicals could be a promising and plausible way to reduce side effects and increase the biocompatibility of inorganic NPs for biomedical applications.     

Metabolism of rumen microbial populations formed on biosubstrates with different assimilation under the effect of pentachlorophenol

It has been established that metabolism of mixed microbial population formed on easy assimilated sources of energy and nitrogen (concentrate diet) progressed on higher level. There is increase of amilolytic activity, formation of lactate, ammonia, low molecular carbonic acids with predomination of propionate molar fraction. The increased resistance to effect of pentachlorophenol (PCP) is characteristic nature of the latter. The role of the most resistant synthrophic bacteria to PCP increases. The pure strains of Streptococcus bovis and Megasphaera elsdenii do not stop metabolism at 100 microM of PCP. Mixed population of microorganisms formed on hard accessible biosubstrates (cellulose) and Butyrivibrio fibrisolvens have the increased cellulosolytic activity and while the high sensibility even to low doses of PCP (10-40 microM) is observed. It has been supposed that mechanism of PCP effect is ambiguous for various species of microbial complex of rumen. It's effect strength on all main chains of metabolism (membrane transport, energetic exchange, protein biosynthesis, etc.) significantly depends on capacity of pool of metabolic intermediates formed as a result of definite program of biotechnology of nurture, but significantly decreases the harmful effect of biocides.     

Demographic effects of road mortality on mammalian populations: a systematic review

In light of rapidly expanding road networks worldwide, there is increasing global awareness of the growing amount of mammalian roadkill. However, the ways in which road mortality affects the population dynamics of different species remains largely unclear. We aimed to categorise the demographic parameters in mammalian populations around the world that are directly or indirectly affected by road mortality, as well as identify the most effective study designs for quantifying population-level consequences of road mortality. We conducted a comprehensive systematic review to synthesise literature published between 2000 and 2021 and out of 11,238 unique studies returned, 83 studies were retained comprising 69 mammalian species and 150 populations. A bias towards research-intensive countries and larger mammals was apparent. Although searches were conducted in five languages, all studies meeting the inclusion criteria were in English. Relatively few studies (13.3%) provided relevant demographic context to roadkill figures, hampering understanding of the impacts on population persistence. We categorised five direct demographic parameters affected by road mortality: sex- and age-biased mortality, the percentage of a population killed on roads per year (values up to 50% were reported), the contribution of roadkill to total mortality rates (up to 80%), and roadkill during inter-patch or long-distance movements. Female-biased mortality may be more prevalent than previously recognised and is likely to be critical to population dynamics. Roadkill was the greatest source of mortality for 28% of studied populations and both additive and compensatory mechanisms to roadkill were found to occur, bringing varied challenges to conservation around roads. In addition, intra-specific population differences in demographic effects of road mortality were common. This highlights that the relative importance of road mortality is likely to be context specific as the road configuration and habitat quality surrounding a population can vary. Road ecology studies that collect data on key life parameters, such as age/stage/sex-specific survival and dispersal success, and that use a combination of methods are critical in understanding long-term impacts. Quantifying the demographic impacts of road mortality is an important yet complex consideration for proactive road management.     

Studies on potential effects of fumaric acid on rumen microbial fermentation,methane production and microbial community

The greenhouse gas methane (CH₄) contributes substantially to global climate change. As a potential approach to decrease ruminal methanogenesis, the effects of different dosages of fumaric acid (FA) on ruminal microbial metabolism and on the microbial community (archaea, bacteria) were studied using a rumen simulation technique (RUSITEC). FA acts as alternative hydrogen acceptor diverting 2H from methanogenesis of archaea towards propionate formation of bacteria. Three identical trials were conducted with 12 fermentation vessels over a period of 14 days. In each trial, four fermentation vessels were assigned to one of the three treatment groups differing in FA dosage: low fumaric acid (LFA), high fumaric acid (HFA) and without FA (control). FA was continuously infused with the buffer. Grass silage and concentrate served as substrate. FA led to decreases in pH and to higher production rates of total short chain fatty acids (SCFA) mediated by increases in propionate for LFA of 1.69 mmol d^?1 and in propionate and acetate production for HFA of 4.49 and 1.10 mmol d^?1, respectively. Concentrations of NH₃-N, microbial crude protein synthesis, their efficiency, degradation of crude nutrients and detergent fibre fraction were unchanged. Total gas and CH₄ production were not affected by FA. Effects of FA on structure of microbial community by means of single strand conformation polymorphism (SSCP) analyses could not be detected. Given the observed increase in propionate production and the unaffected CH₄ production it can be supposed that the availability of reduction equivalents like 2H was not limited by the addition of FA in this study. It has to be concluded from the present study that the application of FA is not an appropriate approach to decrease the ruminal CH₄ production.     

The use of molecular techniques based on ribosomal RNA and DNA for rumen microbial ecosystem studies: a review

This paper analyses the research progress in the use of molecular techniques based on ribosomal RNA and DNA (rRNA/rDNA) for rumen microbial ecosystem since first literature by Stahl et al. (1988). Because rumen microbial populations could be under-estimated by adopting the traditional techniques such as roll-tube technique or most-probable-number estimates, modern molecular techniques based on 16S/18S rRNA/rDNA can be used to more accurately provide molecular characterization, microbe populations and classification scheme than traditional methods. Phylogenetic-group-specific probes can be used to hybridize samples for detecting and quantifying of rumen microbes. But, competitive-PCR and real-time PCR can more sensitively quantify rumen microbes than hybridization. Molecular fingerprinting techniques including both denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and restriction fragment length polymorphisms (RFLP) can used to explore diversity of bacteria, protozoa and fungi in the rumen ecosystem. By constructing clone libraries of 16S/18S rRNA/rDNA of rumen microbes, more new microbes can be discovered and identified. For fungi, internal transcribed spacers (ITS) of fungi are better than 18S rRNA/rDNA for discriminating operational taxonomic units. In conclusion, 16S/18S rRNA/rDNA procedures have been used with success in rumen microbes and are quickly gaining acceptance for studying rumen microbial ecosystem, and will become useful methods for rumen ecology research. However, molecular techniques based on 16S/18S rRNA/rDNA don't preclude classical and traditional microbiological techniques. It should used together to acquire accurate and satisfactory results.     

Dietary effects of fish oils on human health: a review of recent studies

The beneficial effects in humans of ingesting fish oils have attracted much attention among medical scientists and nutritionists recently. Human studies conducted in populations of Eskimos, Japanese, and Caucasians since 1970 are reviewed in this paper. The evidence shows that a diet rich in omega-3 fatty acids significantly reduces plasma cholesterol and triglyceride levels, improves fat tolerance, prolongs bleeding times, reduces platelet counts, and decreases platelet adhesiveness.     

Dietary fat sources affect feed intake,digestibility, rumen microbial populations,energy partition and methane emissions in different beef cattle genotypes

The mitigation of enteric methane emission in beef cattle production is important for reducing feed energy loss and increasing environmental sustainability. The main objective of this study was to evaluate the effect of different oilseeds included in fermented total mixed rations (whole soyabean seed (SBS, control), whole kapok seed (KPS) and cracked oil palm fruit (OPF)) on feed intake, digestibility, rumen microbial populations, energy partition and methane emissions in different cattle genotypes (Charolais crossbred v. Japanese Black crossbred). Three Charolais crossbred and three Japanese Black crossbred bulls were studied in a replicated 3×3 Latin square experimental design; genotypes were analysed in separate squares including three periods of 21 days each and three dietary oilseed treatments fed ad libitum. The cattle were placed in a metabolic cage equipped with a ventilated head box respiration system for evaluating digestibility and energy balance. As compared with Charolais crossbred individuals, Japanese Black crossbred bulls showed consistently lower dry matter intake (15.5%, P<0.01), metabolisable energy (ME) intake (13.8%, P<0.05), ME requirement for maintenance (10.3%; 386 v. 430 kJ/kg metabolic BW, respectively), faeces energy loss (19.2%, P<0.001) and enteric methane emissions (18.5%, P<0.001). However, these two genotypes did not differ in energy retention (ER) (P=0.80). Among the three dietary oilseed treatments, OPF exhibited higher NDF intake (P<0.01) and digestibility (P<0.01), which was associated with a larger (P<0.05) total number of bacteria in the rumen. In addition, the OPF diet contributed to higher ME intake and ER than that of the KPS diet, whereas the SBS diet presented intermediate values (P<0.05). The methane conversion factor of these crossbreds was not significantly affected by genotype (P>0.05) or diet (P>0.05) under the experimental conditions and ranged from 5.8% to 6.0% of gross energy intake. This value is lower than that reported by the Intergovernmental Panel on Climate Change (6.5%) for cattle fed with low-quality crop residues or by-products. Thus, our results imply that the Japanese Black crossbred cattle consume less feed and emits less enteric methane than the Charolais crossbred does, mainly owing to its lower ME requirement for maintenance. The OPF diet could be used to replace SBS for high beef production, although further studies are required to evaluate their application across a wide range of beef production systems.     

The effects of a pesticide program on microbial populations from apple leaf litter

The leaf litter microbial community was quantitatively and qualitatively changed when a standard pesticide schedule that comprised an insecticide, a bactericide, and a fungicide was applied to McIntosh apple trees in the summer. Effects were observed for two winters by four indirect assays and three direct methods. Populations were altered qualitatively both years, but the most striking difference was the quantitative impact from year to year. Bacteria, filamentous fungi, and yeasts from treated leaves were reduced 10- to 10 000-fold between November 1976 and April 1977 and did not recover until snow cover had melted in March. Reductions in 1977-1978 were negligible. The marked seasonal difference is attributed to meteorological influences. Fluorescent pseudomonads were among the bacteria depressed by chemicals. Of the 49 genera of fungi and yeasts isolated, Coniothyrium sp., Penicillium spp., Arthrobotrys spp., and Nodulisporium sp. were appreciably reduced, whereas Typhula spp., Pleurophomella sp., Sporobolomyces spp., and Rhodotorula spp. were substantially enhanced by the spray program.     

乳酸链球菌素对瘤胃体外发酵、甲烷生成及功能菌群数量的影响北大核心CSCD

【目的】旨在通过体外静态模拟瘤胃发酵法研究乳酸链球菌素(NI)对瘤胃发酵、甲烷生成及功能菌群数量的影响。【方法】以不添加任何添加剂处理做阴性对照(NC),以莫能菌素(MON,5μmol/L)做阳性对照,试验组NI添加水平分别为3(NI-3)、9(NI-9)和27 mg/100 m L(NI-27),每个处理4个重复,分别于培养后的0、3、6、9、12、24 h测定产气量和甲烷产量。培养24 h后,采集发酵液样品,用于发酵参数和菌群数量的测定。【结果】与NC组相比,添加NI和MON均能显著降低产气量和甲烷产量(P<0.05);添加NI对pH值、干物质消失率(DMD)和有机物消失率(OMD)无显著影响(P>0.05);NI-9处理组与NC组相比氨态氮浓度显著降低(P<0.05),而NI-3和NI-27组氨氮浓度没有显著变化(P>0.05);相比而言,MON处理组DMD、OMD和氨氮浓度与NC组相比均显著降低(P<0.05),而pH值与其他各处理组相比没有差异(P>0.05);与NC组相比,NI各处理组和MON组乙酸浓度及乙丙比均显著降低(P<0.05),丙酸浓度显著提高(P<0.05)。功能菌方面,qPCR结果显示添加NI和MON对总菌和拟杆菌门数量均无显著影响(P>0.05);与NC相比,添加NI对原虫、甲烷菌、真菌和厚壁菌门数量均无显著影响(P>0.05),而MON组原虫、甲烷菌、真菌和厚壁菌门数量显著降低(P<0.05);NI和MON处理均显著提高了硫还原菌和C.aminophilum数量(P<0.05),但C.sticklandii数量不受影响(P>0.05)。【结论】添加适宜浓度的NI可降低瘤胃甲烷与氨的生成,但并不影响饲料消化,这种发酵模式的改变可能与瘤胃功能菌群数量与多样性的变化密切相关。     

Immune regulatory molecules as modifiers of semen and fertility: A review

Declining fertility rates in both human and animals is a cause for concern. While many of the infertility cases are due to known causes, idiopathic infertility is reported in 30% of the infertile couples. In such cases, 18% of the infertile males carry antisperm antibodies (ASAs). Such data are lacking in livestock, wherein 20–30% of the animals are being culled due to low fertility. In males, the blood–testis barrier (BTB) and biomolecules in the semen provide an immuno‐tolerant microenvironment for spermatozoa as they traverse the immunologic milieu of both the male and female reproductive tracts. For example, insults from environmental contaminants, infections and inflammatory conditions are likely to impact the immune privilege state of the testis and fertility. The female mucosal immune system can recognize allogenic spermatozoa‐specific proteins affecting sperm kinematics and sperm‐zona binding leading to immune infertility. Elucidating the functions and pathways of the immune regulatory molecules associated with fertilization are prerequisites for understanding their impact on fertility. An insight into biomolecules associated with spermatozoal immune tolerance may generate inputs to develop diagnostic tools and modulate fertility. High‐throughput sequencing technologies coupled with bioinformatics analyses provides a path forward to define the array of molecules influencing pregnancy outcome. This review discusses the seminal immune regulatory molecules from their origin in the testis until they traverse the uterine environment enabling fertilization and embryonic development. Well‐designed experiments and the identification of biomarkers may provide a pathway to understand the finer details of reproductive immunology that will afford personalized therapies.     

The interactive effects of plant microbial symbionts: a review and meta-analysis

In nature, plants often associate with multiple symbionts concurrently, yet the effects of tripartite symbioses are not well understood. We expected synergistic growth responses from plants associating with functionally distinct symbionts. In contrast, symbionts providing similar benefits to a host may reduce host plant growth. We reviewed studies investigating the effect of multiple interactions on host plant performance. Additionally, we conducted a meta-analysis on the studies that performed controlled manipulations of the presence of two microbial symbionts. Using response ratios, we investigated the effects on plants of pairs of symbionts (mycorrhizal fungi, fungal endophytes, and nitrogen-fixers). The results did not support the view that arbuscular mycorrhizal (AM) fungi and rhizobia should interact synergistically. In contrast, we found the joint effects of fungal endophytes and arbuscular mycorrhizal fungi to be greater than expected given their independent effects. This increase in plant performance only held for antagonistic endophytes, whose negative effects were alleviated when in association with AM fungi, while the impact of beneficial endophytes was not altered by infection with AM fungi. Generalizations from the meta-analysis were limited by the substantial variation within types of interactions and the data available, highlighting the need for more research on a range of plant systems.     

Biofilms as a microbial hazard in the food industry: A scoping review

Biofilms pose a serious public health hazard with a significant economic impact on the food industry. The present scoping review is designed to analyse the literature published during 2001–2020 on biofilm formation of microbes, their detection methods, and association with antimicrobial resistance (if any). The peer-reviewed articles retrieved from 04 electronic databases were assessed using PRISMA-ScR guidelines. From the 978 preliminary search results, a total of 88 publications were included in the study. On analysis, the commonly isolated pathogens were Listeria monocytogenes, Staphylococcus aureus, Salmonella spp., Escherichia coli, Bacillus spp., Vibrio spp., Campylobacter jejuni and Clostridium perfringens. The biofilm-forming ability of microbes was found to be influenced by various factors such as attachment surfaces, temperature, presence of other species, nutrient availability etc. A total of 18 studies characterized the biofilm-forming genes, particularly for S. aureus, Salmonella spp., and E. coli. In most studies, polystyrene plate and/or stainless-steel coupons were used for biofilm formation, and the detection was carried out by crystal violet assays and/or by plate counting method. The strain-specific significant differences in biofilm formation were observed in many studies, and few studies carried out analysis of multi-species biofilms. The association between biofilm formation and antimicrobial resistance was not clearly defined. Further, viable but non-culturable form of the foodborne pathogens is posing an unseen (by conventional cultivation techniques) but potent threat to the food safety. The present review recommends the need for carrying out systematic surveys and risk analysis of biofilms in food chain to highlight the evidence-based public health concerns, especially in regions where microbiological food hazards are quite prevalent.     

持留菌及其对微生物膜的耐受性影响研究进展

持留菌（persisters）是细菌种群中所占比例不到0.1%的一类特殊亚群,具有与种群内普通菌、抗性突变菌所不同的特征,其形成机制复杂,不易分离培养.持留菌可通过“休眠-生长-增殖”应对逆境的胁迫,维持自身生存和菌体结构稳定,在生物膜的多药耐受性与多金属耐性中发挥着重要作用,对于维持微生物群落结构稳定具有重要意义.本文从持留菌的研究历程、特点、基因调控机制及其对微生物膜的耐药性与多金属耐性的影响等方面进行了综述,并对今后的研究方向进行了展望.     

Heterogeneity as an adaptive trait of microbial populations

The review deals with heterogeneity of bacterial populations, a superorganismic characteristic providing for their adaptation to environmental conditions at the population-communication level. This phenomenon attracts increasing attention as an example of collective forms of microbial behavior and the mechanisms of cell survival in communities. Heterogeneity of bacterial populations may be discrete or continuous and may result from both phenotypic and genotypic variations. Heterogeneity of microbial cells results from the interaction of internal and environmental factors, as well as from random fluctuations of the biochemical and physiological characteristics. Cell heterogeneity improves the survival of bacterial populations under heterogeneous or variable environmental conditions, as well as under the effect of stress factors. This phenomenon should be taken into account for the development of strategies for cultivation of the biotechnologically important microorganisms and for the rational therapy of infections.     

Protection against chemotherapy- and radiotherapy-induced side effects: A review based on the mechanisms and therapeutic opportunities of phytochemicals

BackgroundAlthough great achievements have been made in the field of cancer therapy, chemotherapy and radiotherapy remain the mainstay cancer therapeutic modalities. However, they are associated with various side effects, including cardiocytotoxicity, nephrotoxicity, myelosuppression, neurotoxicity, hepatotoxicity, gastrointestinal toxicity, mucositis, and alopecia, which severely affect the quality of life of cancer patients. Plants harbor a great chemical diversity and flexible biological properties that are well-compatible with their use as adjuvant therapy in reducing the side effects of cancer therapy.PurposeThis review aimed to comprehensively summarize the molecular mechanisms by which phytochemicals ameliorate the side effects of cancer therapies and their potential clinical applications.MethodsWe obtained information from PubMed, Science Direct, Web of Science, and Google scholar, and introduced the molecular mechanisms by which chemotherapeutic drugs and irradiation induce toxic side effects. Accordingly, we summarized the underlying mechanisms of representative phytochemicals in reducing these side effects.ResultsRepresentative phytochemicals exhibit a great potential in reducing the side effects of chemotherapy and radiotherapy due to their broad range of biological activities, including antioxidation, antimutagenesis, anti-inflammation, myeloprotection, and immunomodulation. However, since a majority of the phytochemicals have only been subjected to preclinical studies, clinical trials are imperative to comprehensively evaluate their therapeutic values.ConclusionThis review highlights that phytochemicals have interesting properties in relieving the side effects of chemotherapy and radiotherapy. Future studies are required to explore the clinical benefits of these phytochemicals for exploitation in chemotherapy and radiotherapy.