Ruminant Salivary Microbes: Passenger or Player in the Rumen?

Sampling of ruminant saliva has gained interest as a non-invasive proxy for exploring the structure of the rumen microbiome. However, the subsequent data analysis assumes that bacteria originating from the oral cavity are merely passengers in the rumen and play no active role. In this study, it was hypothesised that metabolically active oral bacteria present in the salivary microbiome play a role in the ruminal degradation of plant material. In vitro cultivation-based enumeration confirmed that the ruminant oral cavity harbours a significant number of anaerobic and cellulolytic bacteria that are metabolically active under ruminal conditions. Bacterial 16S rRNA gene profiling of in vitro enrichments also confirmed that oral-derived bacteria were capable of colonising plant material. Preliminary analysis of the colonising bacteria indicated that bacteria belonging to the genus Streptococcus were of particular interest. In conclusion, the findings of the current study clearly indicate that bolus-associated bacteria have the potential to play a metabolically active role in terms of ruminal colonisation and the degradation of plant material. This evidence confirms the merit of the hypothesis that the metabolically active oral bacteria present in the salivary microbiome may play a role in the ruminal degradation of plant material.

Prepartum Magnesium Butyrate Supplementation of Dairy Cows Improves Colostrum Yield, Calving Ease, Fertility, Early Lactation Performance and Neonatal Vitality.

Butyrate promotes rumen epithelium growth and function; however, the effect of prepartum butyrate supplementation on dairy cow productivity, health and their offspring has not been extensively studied. Furthermore, no studies have investigated the effect of magnesium butyrate (MgB), which is also a source of magnesium. A trial was performed to test the hypothesis that prepartum MgB supplementation (105 g/cow/day) would increase colostrum quality and improve calving, newborn calf vitality and cow health. Multiparous Holstein cows were randomly assigned to MgB supplemented (n = 107) and Control groups (n = 112). Colostrum yield and the total yield of IgG, protein and lactose were higher (p ≤ 0.05) in the supplemented group. The calving assistance rate was lower (p ≤ 0.012), and the neonatal vitality score was higher (p ≤ 0.001) in the MgB group. Improved parameters related to cow health and fertility were observed in the supplemented group. The MgB group also had higher milk yield during the first week of lactation (p ≤ 0.001), and a higher (p ≤ 0.05) body condition score from 3 to 9 weeks after calving. In conclusion, prepartum MgB supplementation provides a wide range of benefits for dairy cows, as well as their newborn calves.

Dietary Protected Butyrate Supplementation of Broilers Modulates Intestinal Tight Junction Proteins and Stimulates Endogenous Production of Short Chain Fatty Acids in the Caecum.

Short chain fatty acid (SCFA) butyrate has various beneficial effects on the gut microbiota as well as on the overall health status and metabolism of the host organism. The modulatory role of butyrate on gut barrier integrity reflected by tight junction protein expression has been already described in mammalian species. However, there is limited information available regarding chickens. Therefore, the main aim of this study was to monitor the effects of protected butyrate on claudin barrier protein and monocarboxylate transporter 1 abundance in different gastrointestinal segments of chickens as well as the growth performance of broiler chickens. The effect of protected butyrate on the caecal microbiota was monitored by quantifying the concentrations of total eubacteria and key enzymes of butyrate production. Furthermore, intestinal SCFA concentrations were also measured. Based on the data obtained, protected butyrate increased the overall performance as well as the barrier integrity of various gut segments. Protected butyrate also positively affected the SCFA concentration and composition. These findings provide valuable insight into the complex effects of protected butyrate on broiler gut health, highlighting the beneficial effects in improving intestinal barrier integrity and performance parameters.

Characterization and rank assignment criteria for the anaerobic fungi (Neocallimastigomycota).

Establishing a solid taxonomic framework is crucial for enabling discovery and documentation efforts. This ensures effective communication between scientists as well as reproducibility of results between laboratories, and facilitates the exchange and preservation of biological material. Such framework can only be achieved by establishing clear criteria for taxa characterization and rank assignment. Within the anaerobic fungi (phylum Neocallimastigomycota), the need for such criteria is especially vital. Difficulties associated with their isolation, maintenance and long-term storage often result in limited availability and loss of previously described taxa. To this end, we provide here a list of morphological, microscopic, phylogenetic and phenotypic criteria for assessment and documentation when characterizing newly obtained Neocallimastigomycota isolates. We also recommend a polyphasic rank-assignment scheme for novel genus-, species- and strain-level designations for newly obtained Neocallimastigomycota isolates.

Reproductive decision-making of Black women living with HIV: A systematic review.

BACKGROUND: Black women living with HIV account for a higher proportion of new HIV diagnoses than other groups. These women experience restricted access to reproductive services and inadequate support from healthcare providers because their position in society is based on their sexual health and social identity in the context of this stigmatizing chronic disease. By recognizing the analytical relevance of intersectionality, the reproductive decision-making of Black women can be explored as a social phenomenon of society with varied positionality. OBJECTIVE: The purpose of this review was to synthesize the evidence about the reproductive decision-making of Black women living with HIV in high-income countries from the beginning of the HIV epidemic to the present. METHODS: This systematic review was guided by the JBI evidence synthesis recommendations. Searches were completed in seven databases from 1985 to 2021, and the review protocol was registered with PROSPERO (CRD420180919). RESULTS: Of 3503 records, 22 studies were chosen for synthesis, including 19 observational and three qualitative designs. Nearly, all studies originated from the United States; the earliest was reported in 1995. Few studies provided detailed sociodemographic data or subgroup analysis focused on race or ethnicity. Influencing factors for reproductive decision-making were organized into the following seven categories: ethnicity, race, and pregnancy; religion and spirituality; attitudes and beliefs about antiretroviral therapy; supportive people; motherhood and fulfillment; reproductive planning; and health and wellness. CONCLUSION: No major differences were identified in the reproductive decision-making of Black women living with HIV. Even though Black women were the largest group of women living with HIV, no studies reported a subgroup analysis, and few studies detailed sociodemographic information specific to Black women. In the future, institutional review boards should require a subgroup analysis for Black women when they are included as participants in larger studies of women living with HIV.

Free Faecal Water: Analysis of Horse Faecal Microbiota and the Impact of Faecal Microbial Transplantation on Symptom Severity.

Free faecal water (FFW) in equines results in pollution of the hindquarters and tail and can also involve clinical signs. Though the cause of FFW is unknown, it was hypothesized that it may involve the gut microbiota. This hypothesis was addressed as follows. First, the faecal prokaryotic community composition of horses suffering from FFW relative to healthy controls (n = 10) was compared. Second, FFW horses were treated with a standardised faecal microbiota transplantation (FMT) protocol (n = 10), followed by assessment of FFW symptom severity and faecal prokaryotic community composition over a follow-up period of 168 days. No significant differences were found in the faecal microbiota composition of FFW horses compared to healthy controls (p > 0.05). Relative to before FMT, FFW symptom severity decreased in affected horses 14 days after FMT (p = 0.02) and remained decreased for the remainder of the study (p < 0.02). However, individual animal responses to FMT varied. FMT had no effect on FFW horse faecal prokaryotic community composition in terms of alpha or beta diversity. Alpha diversity of the donor inocula used in the FMT was always lower than that of the faecal microbiota of the FFW treated horses (p < 0.001). In conclusion, whilst findings indicate FFW horses do not have an altered hindgut microbiota, some horses that received FMT had a temporary alleviation of FFW symptom severity without causing changes in the faecal microbiota. Future studies using controls are now needed to confirm the effectiveness of FMT to treat FFW.

Motherhood and decision-making among women living with HIV in developed countries: a systematic review with qualitative research synthesis.

BACKGROUND: Women living with HIV (WLH) lack evidence-based information about reproductive options while managing pressures from family, clinicians, and communities to give up the idea of having children. As the reproduction intentions of WLH are not well understood, stigmatizing behaviors force them to hide their disease to avoid rejection by their family, partner, and social networks. Compliance with social norms, fear of stigma, and discrimination influence their experience. Current research is individual qualitative studies lacking the synthesis perspective necessary to guide intervention development. The purpose of this study was to synthesize the evidence to explain the reproductive decision-making process for WLH in developed countries. METHODS: A systematic review with qualitative research synthesis was conducted through searches in 10 electronic databases (CINAHL, EMBASE, MEDLINE, Scopus, Social Science Citation Index, Web of Science, Google Scholar, Cuidatge, Cuiden Enfispo, and SciELO). Studies published in journals from 1995 to 2019 with qualitative data about reproductive decision-making among WLH in developed countries were eligible for inclusion. Developed country was operationalized by membership in the OECD for comparative conditions of social wellbeing and economic stability. The CASP and JBI checklists for qualitative research were used to assess study quality and methodological integrity. Thematic analysis and qualitative meta-summary techniques were used for the synthesis. RESULTS: Twenty studies from 12 developed countries were included in the synthesis. Findings were organized into 3 meta-themes from 15 themes and 45 subthemes, including: (1) Shattered identity, (2) Barriers, inequities, and misinformation, (3) Coping, resiliency, and support. Reproductive decision-making was perceived as a complex process influenced by facilitators and barriers. The facilitators helped WLH cope with their new situation to become more resilient, while the barriers made their situation more difficult to manage. CONCLUSION: WLH encounter reproductive decision-making with knowledge deficits and limited social support. An integrated approach to holistic care with comprehensive multidisciplinary counseling is needed to support WLH. Clinicians could benefit from professional development to learn how to be authentically present for WLH, including engaging in conversations, demonstrating compassion, and understanding situations. Evidence-based clinical practice guidelines need to be tailored for the family planning and sexual health needs of WLH.

RESUMEN: ANTECEDENTES: Las mujeres que viven con el VIH (MVV) carecen de información basada en evidencias sobre las opciones reproductivas mientras son presionadas por la familia, los profesionales de la salud y los miembros de la comunidad para renunciar a la idea de tener hijos. Como las intenciones reproductivas de las MVV no son comprendidas, las conductas estigmatizantes las obligan a ocultar su enfermedad para evitar el rechazo de su familia, pareja y grupos sociales. El cumplimiento de las normas sociales, el miedo al estigma y la discriminación influyen en su experiencia. La presente investigación está compuesta por estudios cualitativos que de forma individual carecen de la perspectiva de síntesis necesaria para guiar el desarrollo de las intervenciones. El propósito de este estudio fue sintetizar la evidencia para explicar el proceso de toma de decisiones reproductivas para las MVV en los países desarrollados. MéTODOS: Se realizó una revisión sistemática con síntesis de investigación cualitativa mediante búsquedas en 10 bases de datos electrónicas (CINAHL, EMBASE, MEDLINE, Scopus, Social Science Citation Index, Web of Science, Google Scholar, Cuidatge, Cuiden Enfispo y SciELO). Los estudios publicados en revistas de entre 1995 y 2019 que contuvieran datos cualitativos sobre la toma de decisiones reproductivas entre las MVV en países desarrollados fueron elegibles para su inclusión. Se consideraron países desarrollados aquellos que pertenecieran a la OCDE con el objetivo de comparar condiciones de bienestar social y estabilidad económica. Las listas de verificación CASP y JBI para la investigación cualitativa se utilizaron para evaluar la calidad del estudio y la integridad metodológica. Para la síntesis se utilizaron técnicas de análisis temático y metanálisis cualitativo. RESULTADOS: En la síntesis se incluyeron veinte estudios de 12 países desarrollados. Los hallazgos se organizaron en 3 metatemas de 15 temas y 45 subtemas, incluyendo: (1) Identidad fragmentada, (2) Barreras, inequidades y desinformación, (3) Afrontamiento, resiliencia y apoyo. La toma de decisiones reproductivas se percibió como un proceso complejo influenciado por factores facilitadores y barrera. Los facilitadores ayudaron a las MVV a afrontar su nueva realidad para volverse más resilientes, mientras que las barreras hicieron que su situación fuera más difícil de manejar. CONCLUSIóN: Las MVV enfrentan la toma de decisiones reproductivas con déficits de conocimiento y apoyo social limitado. Es necesario adoptar un enfoque holístico de atención integral con asesoramiento multidisciplinario para acompañar a las MVV. Los clínicos podrían beneficiarse del desarrollo profesional para aprender a estar verdaderamente presentes para las MVV, participando en reflexiones, demostrando compasión y comprendiendo sus situaciones. Las guías de práctica clínica basadas en la evidencia deben adaptarse a las necesidades de planificación familiar y salud sexual y reproductiva de las MVV. Plain Language Summary Women living with HIV can become pregnant and deliver a healthy baby due to advances in medicine. Being a mother is an important role that gives meaning to life for most women. For women living with HIV thinking about having a baby is difficult because HIV complicates many areas of daily living. When women living with HIV try to speak with physicians and nurses about having a baby, they often do not feel supported and report feeling stigmatized. This review of the scientific literature summarizes the experiences of women living with HIV in developed countries as they considered having a baby. Ten electronic databases were searched for studies published between 1995 and 2019 reporting interviews with women living with HIV about becoming pregnant and having a baby. From the 4519 articles identified, 20 were included for review with 1395 participants from 12 developed countries. After abstracting and analyzing the interviews, three themes were developed to summarize the process described by women living with HIV as they considered pregnancy and the possibility of having a baby, including: (1) Shattered identity, (2) Barriers, inequities, and misinformation, and (3) Coping, resiliency, and support. When women living with HIV consider having a baby, they need to feel comfortable and safe speaking with physicians and nurses about family planning. They also need more support from their partner, as well as family and friends. Strategies need to be implemented to improve the family planning process for women living with HIV, including education health care providers about speaking to women about pregnancy and having a healthy baby.

Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches.

BACKGROUND: Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh perennial ryegrass (PRG)-biofilm interface in the rumen using an in sacco approach and prokaryotic metatranscriptomic profiling. RESULTS: Network analysis identified two distinct sub-microbiomes primarily representing primary (≤ 4 h) and secondary (≥ 4 h) colonisation phases and the most transcriptionally active bacterial families (i.e Fibrobacteriaceae, Selemondaceae and Methanobacteriaceae) did not interact with either sub-microbiome, indicating non-cooperative behaviour. Conversely, Prevotellaceae had most transcriptional activity within the primary sub-microbiome (focussed on protein metabolism) and Lachnospiraceae within the secondary sub-microbiome (focussed on carbohydrate degradation). Putative keystone taxa, with low transcriptional activity, were identified within both sub-microbiomes, highlighting the important synergistic role of minor bacterial families; however, we hypothesise that they may be 'cheating' in order to capitalise on the energy-harvesting capacity of other microbes. In terms of chemical cues underlying transition from primary to secondary colonisation phases, we suggest that AI-2-based quorum sensing plays a role, based on LuxS gene expression data, coupled with changes in PRG chemistry. CONCLUSIONS: In summary, we show that fresh PRG-attached prokaryotes are resilient and adapt quickly to changing niches. This study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen. The study also provides valuable insights into potential plant breeding strategies for development of the utopian plant, allowing optimal sustainable production of ruminants. Video Abstract.

The meaning of postpartum sexual health for women living in Spain: a phenomenological inquiry.

BACKGROUND: Sexual health is a multidimensional phenomenon constructed by personal, social, and cultural factors but continues to be studied with a biomedical approach. During the postpartum period, a woman transitions to mother, as well as partner-to-parent and couple-to-family. There are new realities in life in the postpartum period, including household changes and new responsibilities that can impact the quality of sexual health. This phenomenon is understudied especially in the context of Spain. The purpose of this study was to describe the lived experience of postpartum sexual health among primiparous women giving birth in Catalonia (Spain). METHODS: This was a phenomenological study with a purposive sample of primiparous women. Data was collected through semi-structured interviews until saturation. Analysis followed Colaizzi's seven-step process with an eighth translation step added to limit cross-cultural threats to validity. Also, the four dimensions of trustworthiness were established through strategies and techniques during data collection and analysis. RESULTS: Ten women were interviewed from which five themes emerged, including: Not feeling ready, inhibiting factors, new reality at home, socio-cultural factors, and the clinician within the health system. Returning to sexual health led women to engage in experiential learning through trial and error. Most participants reported reduced libido, experienced altered body image, and recounted resumption of sexual activity before feeling ready. A common finding was fatigue and feeling overloaded by the demands of the newborn. Partner support was described as essential to returning to a meaningful relationship. Discussions about postpartum sexual health with clinicians were described as taboo, and largely absent from the care model. CONCLUSION: Evidence-based practices should incorporate the best evidence from research, consider the postpartum sexual health experiences and preferences of the woman, and use clinician expertise in discussions that include the topic of postpartum sexual health to make decisions. As such, human caring practices should be incorporated into clinical guidelines to recognize the preferences of women. Clinicians need to be authentically present, engage in active communication, and individualize their care. More qualitative studies are needed to understand postpartum sexual health in different contexts, cultures, and countries and to identify similarities and differences through meta-synthesis.

Anaerobic Fungi: Past, Present, and Future.

Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent marker-gene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed -omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.

Increasing the Sustainability of Maize Grain Production by Using Arbuscular Mycorrhizal Fungi Does Not Affect the Rumen of Dairy Cattle (Bos taurus) and Buffalo (Bubalus bubalis).

New approaches are needed to improve the sustainability of feed production and utilization by ruminants. Promising approaches include increased use of buffaloes for more sustainable milk production, and arbuscular mycorrhizal fungi (AMF) to reduce crop production input needs. However, studies assessing the effect of crops grown in the presence of AMF on rumen microbial utilization are limited. Based on current knowledge, we hypothesized that maize grain grown on AMF-inoculated soil affected ruminal fermentation and microbiota, and that this effect differed between buffalo and cattle. A dietary cross-over study (four weeks per diet) was conducted using rumen-cannulated cattle (n = 5) and buffalo (n = 6) to assess the effect of maize grain (3.9% (w/v) of diet) grown on soil with or without AMF (15 kg/ha) on ruminal fermentation and microbiota. Production of maize on AMF-treated soil did not affect any of the assessed ruminal fermentation parameters, microbial concentrations, or prokaryotic community composition (using prokaryotic 16S rRNA gene sequence analysis). In contrast, host type had numerous effects. Protozoal counts, lactate, total VFA and isobutyrate, were significantly higher in buffaloes compared to cattle. Conversely, butyrate was significantly lower in buffaloes than in cattle. Host type explained 9.3% of the total variation in prokaryotic community composition, and relative abundance of nine amplicon sequence variants significantly differed between host types. These findings indicate that AMF treatment of maize crops has no detrimental impact on the value of the resulting maize grains as a ruminant feed, and provides additional insight into rumen-based differences between cattle and buffalo.

Cut-Lengths of Perennial Ryegrass Leaf-Blades Influences In Vitro Fermentation by the Anaerobic Fungus Neocallimastix frontalis.

Anaerobic fungi in the gut of domesticated and wild mammalian herbivores play a key role in the host's ability to utilize plant biomass. Due to their highly effective ability to enzymatically degrade lignocellulose, anaerobic fungi are biotechnologically interesting. Numerous factors have been shown to affect the ability of anaerobic fungi to break down plant biomass. However, methods to reduce the non-productive lag time in batch cultures and the effect of leaf-blade cut-length and condition on the fungal fermentation are not known. Therefore, experimentation using a novel gas production approach with pre-grown, axenic cultures of Neocallimastix frontalis was performed using both fresh and air-dried perennial ryegrass leaf-blades of different cut-lengths. The methodology adopted removed the lag-phase and demonstrated the digestion of un-autoclaved leaf-blades. Fermentation of leaf-blades of 4.0 cm cut-length produced 18.4% more gas yet retained 11.2% more apparent DM relative to 0.5 cm cut-length leaf-blades. Drying did not affect fermentation by N. frontalis, although an interaction between drying and leaf-blade cut-length was noted. Removal of the lag phase and the use of un-autoclaved substrates are important when considering the biotechnological potential of anaerobic fungi. A hypothesis based upon sporulation at cut surfaces is proposed to describe the experimental results.

Characterization of dairy cow rumen bacterial and archaeal communities associated with grass silage and maize silage based diets.

The objective of the present study was to characterize the rumen bacterial and archaeal communities in dairy cows fed different ratios of maize silage (MS) and grass silage (GS), and place the findings in the context of ruminal fermentation as well as previously reported methane (CH4) emissions. Rumen fluid from 12 rumen cannulated dairy cows was collected after 10 and 17 days of feeding one of four diets, all of which had the same roughage to concentrate ratio of 80:20 based on dry matter (DM). Roughage in the four diets (GS100, GS0, GS67, GS33) consisted of either 1000 g/kg DM GS (GS100), 1000 g/kg DM MS (GS0), or a mixture of both silages in different proportions [667 g/kg DM GS and 333 g/kg DM MS (GS67); 333 g/kg DM GS and 677 g/kg DM MS (GS33)]. Total volatile fatty acid (VFA) concentrations and the molar proportions of the ruminal VFA were not affected by diet. Only the molar proportion of isovalerate was affected by time, being lower on day 17 than on day 10. Bacterial and archaeal concentrations were not affected by diet but increased from day 10 to day 17. The bacterial community composition was affected by diet, time and diet × time, whereas the archaeal community composition was only affected by diet. Several bacterial and archaeal genus level groups were associated with diet, but not with time. Analysis indicated the increased use of hydrogen by succinate and lactate producing bacteria is likely to at least partially explain the previously reported lower CH4 emissions from MS fed dairy cows. Furthermore, time had a significant effect on both bacterial and archaeal concentrations, and also bacterial community composition. This indicates that the rumen microbiota had not stabilized after 10 days of feeding the experimental diets.

Faculty Attitudes About Caring for People Living With HIV/AIDS: A Comparative Study.

BACKGROUND: People living with HIV/AIDS (PLHIV) experience stigma and discrimination. Negative attitudes of nursing faculty about caring for PLHIV can adversely affect student perceptions and their nursing care. The study purpose was to describe nursing faculty attitudes and beliefs about caring for PLHIV. METHOD: The HPASS (Healthcare Provider HIV/AIDS Stigma Scale), Spanish version, was delivered to nursing faculty in Colombia and Peru. RESULTS: The HPASS was completed by 98 nursing faculty. The overall mean score was 2.41 (SD = 0.69), with subscale scores: stereotypes, 2.55 (SD = 0.84); discrimination, 2.28 (SD = 0.74); and prejudices, 2.41 (SD = 0.63). Peruvian faculty had the highest scores, statistically correlated with the importance of religion, whereas Colombia had the lowest. CONCLUSION: Nursing faculty attitudes toward PLHIV were slightly positive in Colombia to slightly negative in Peru; however, both countries had negative stereotypes. Knowledge deficiencies about HIV persist and attitudes appear to be influenced by culture and religion. [J Nurs Educ. 2019;58(12):712-717.].

Differently Pre-treated Alfalfa Silages Affect the in vitro Ruminal Microbiota Composition.

Alfalfa (Medicago sativa L.) silage (AS) is an important feedstuff in ruminant nutrition. However, its high non-protein nitrogen content often leads to poor ruminal nitrogen retention. Various pre-ensiling treatments differing with respect to dry matter concentrations, wilting intensities and sucrose addition have been previously shown to improve the quality and true protein preservation of AS, and have substantial effects on in vitro ruminal fermentation of the resulting silages. However, it is unknown how these pre-ensiling treatments affect the ruminal microbiota composition, and whether alterations in the microbiota explain previously observed differences in ruminal fermentation. Therefore, during AS incubation in a rumen simulation system, liquid and solid phases were sampled 2 and 7 days after first incubating AS, representing an early (ET) and late (LT) time point, respectively. Subsequently, DNA was extracted and qPCR (bacteria, archaea, and anaerobic fungi) and prokaryotic 16S rRNA gene amplicon sequence analyses were performed. At the ET, high dry matter concentration and sucrose addition increased concentrations of archaea in the liquid phase (P = 0.001) and anaerobic fungi in the solid phase (P < 0.001). At the LT, only sucrose addition increased archaeal concentration in the liquid phase (P = 0.014) and anaerobic fungal concentration in the solid phase (P < 0.001). Bacterial concentrations were not affected by pre-ensiling treatments. The prokaryotic phylogenetic diversity index decreased in the liquid phase from ET to LT (P = 0.034), whereas the solid phase was not affected (P = 0.060). This is suggestive of a general adaption of the microbiota to the soluble metabolites released from the incubated AS, particularly regarding the sucrose-treated AS. Redundancy analysis of the sequence data at the genus level indicated that sucrose addition (P = 0.001), time point (P = 0.001), and their interaction (P = 0.001) affected microbial community composition in both phases. In summary, of the pre-ensiling treatments tested sucrose addition had the largest effect on the microbiota, and together with sampling time point affected microbiota composition in both phases of the rumen simulation system. Thus, microbiota composition analysis helped to understand the ruminal fermentation patterns, but could not fully explain them.

Assessment of the Accuracy of High-Throughput Sequencing of the ITS1 Region of Neocallimastigomycota for Community Composition Analysis.

Anaerobic fungi (Neocallimastigomycota) are common inhabitants of the digestive tract of large mammalian herbivores, where they make an important contribution to plant biomass degradation. The internal transcribed spacer 1 (ITS1) region is currently the molecular marker of choice for anaerobic fungal community analysis, despite its known size polymorphism and heterogeneity. The aim of this study was to assess the accuracy of high-throughput sequencing of the ITS1 region of anaerobic fungi for community composition analysis. To this end, full-length ITS1 clone libraries from five pure cultures, representing the ITS1 region size range, were Sanger sequenced to generate a reference dataset. Barcoded amplicons of the same five pure cultures, and four different mock communities derived from them, were then sequenced using Illumina HiSeq. The resulting sequences were then assessed in relation to either the reference dataset (for the pure cultures) or the corresponding theoretical mock communities. Annotation of sequences obtained from individual pure cultures was not always consistent at the clade or genus level, irrespective of whether data from clone libraries or high-throughput sequencing were analyzed. The detection limit of the high-throughput sequencing method appeared to be influenced by factors other than the parameters used during data processing, as some taxa with theoretical values >0.6% were not detected in the mock communities. The high number of PCR cycles used was considered to be a potential explanation for this observation. Accuracy of two of the four mock communities was limited, and this was speculated to be due to preferential amplification of smaller sized ITS1 regions. If this is true, then this is predicted to be an issue with only six of the 32 named anaerobic fungal clades. Whilst high-throughput sequencing of the ITS1 region from anaerobic fungi can be used for environmental sample analysis, we conclude that the accuracy of the method is influenced by sample community composition. Furthermore, ambiguity in the annotation of sequences within pure cultures due to ITS1 heterogeneity reinforces the limitations of the ITS1 region for the taxonomic assignment of anaerobic fungi. In order to overcome these issues, there is a need to develop an alternative taxonomic marker for anaerobic fungi.

Adherence to antiretroviral therapy and the associated factors among people living with HIV/AIDS in Northern Peru: a cross-sectional study.

BACKGROUND: There are approximately 72,000 people living with HIV/AIDS (PLHIV) in Peru. Non-adherence to antiretroviral therapy (ART) is the most important factor for therapeutic failure and the development of resistance. Peru has achieved moderate progress in meeting the 90-90-90 targets, but only 60% of PLHIV receiving ART are virally suppressed. The purpose of this study was to understand ART adherence in the Peruvian context, including developing sociodemographic and clinical profiles, evaluating the clinical management strategies, and analyzing the relationships between the variables and adherence of PLHIV managed at a regional HIV clinic in Lambayeque Province (Northern Peru). METHODS: This was a cross-sectional study with 180 PLHIV adults, non-randomly but consecutively selected with self-reported ART compliance (78.2% of the eligible population). The PLHIV profile (PLHIV-Pro) and the Simplified Medication Adherence Questionnaire (SMAQ) were used to collect sociodemographic information, clinical variables, and data specific to ART adherence. Descriptive analysis of sociodemographic and clinical characteristics was performed. Bivariate analysis was performed with the Mann-Whitney test, Chi square test, and Yates correction. RESULTS: The 180 PLHIV sample included 78.9% men, 49.4% heterosexual, 45% with a detectable HIV-1 viral load less than 40 copies/ml, 58.3% not consistently adherent, and only 26.1% receiving Tenofovir + Lamivudine + Efavirenz. Risk factors significant for non-adherence included concurrent tuberculosis, discomfort with the ART regime, and previous pauses in ART. Multivariate analysis of nested models indicated having children is a protector factor for adherence. CONCLUSIONS: Self-reported adherence appeared to be low and the use of first-line therapy is not being prescribed homogeneously. Factors associated with nonadherence are both medical and behavioral, such as having tuberculosis, pausing ART, or experiencing discomfort with ART. The Peruvian government needs to update national technical standards, monitor medication availability, and provide education to health care professionals in alignment with evidence-based guidelines and international recommendations. Instruments to measure adherence need to be developed and evaluated for use in Latin America.

Metatranscriptomics reveals mycoviral populations in the ovine rumen.

The rumen is known to contain DNA-based viruses, although it is not known whether RNA-based viruses that infect fungi (mycoviruses) are also present. Analysis of publicly available rumen metatranscriptome sequence data from sheep rumen samples (n = 20) was used to assess whether RNA-based viruses exist within the ovine rumen. A total of 2466 unique RNA viral contigs were identified that had homology to nine viral families. The Partitiviridae was the most consistently observed mycoviral family. High variation in the abundance of each detected mycovirus suggests that rumen mycoviral populations vary greatly between individual sheep. Functional analysis of the genes within the assembled mycoviral contigs suggests that the mycoviruses detected had simple genomes, often only carrying the machinery required for replication. The fungal population of the ovine rumen was also assessed using metagenomics data from the same samples, and was consistently dominated by the phyla Ascomycota and Basidomycota. The strictly anaerobic phyla Neocallimastigomycota were also present in all samples but at a low abundance. This preliminary investigation has provided clear evidence that mycoviruses with RNA genomes exist in the rumen, with further in-depth studies now required to characterise this mycoviral community and determine its role in the rumen.