Bacterial Alpha Diversity Research Articles

The Arctic summer microbiome across Fram Strait: Depth, longitude, and substrate concentrations structure microbial diversity in the euphotic zone.

The long-term dynamics of microbial communities across geographic, hydrographic, and biogeochemical gradients in the Arctic Ocean are largely unknown. To address this, we annually sampled polar, mixed, and Atlantic water masses of the Fram Strait (2015-2019; 5-100 m depth) to assess microbiome composition, substrate concentrations, and oceanographic parameters. Longitude and water depth were the major determinants (~30%) of microbial community variability. Bacterial alpha diversity was highest in lower-photic polar waters. Community composition shifted from west to east, with the prevalence of, for example, Dadabacteriales and Thiotrichales in Arctic- and Atlantic-influenced waters, respectively. Concentrations of dissolved organic carbon peaked in the western, compared to carbohydrates in the chlorophyll-maximum of eastern Fram Strait. Interannual differences due to the time of sampling, which varied between early (June 2016/2018) and late (September 2019) phytoplankton bloom stages, illustrated that phytoplankton composition and resulting availability of labile substrates influence bacterial dynamics. We identified 10 species clusters with stable environmental correlations, representing signature populations of distinct ecosystem states. In context with published metagenomic evidence, our microbial-biogeochemical inventory of a key Arctic region establishes a benchmark to assess ecosystem dynamics and the imprint of climate change.

P118 Fecal content from IBD patients disturbs epithelial functions in two model systems

Abstract Background Inflammatory Bowel Diseases (IBD) result from abnormal interactions between the immune system, epithelial barrier, and gut microbiota. However, understanding the abnormal interaction between aerobic epithelia and mainly anaerobic microbiota is complicated and is limited in part by the lack of human-relevant models. Methods We developed a model system that is based on whole human fecal samples and human-derived epithelia to study the interactions between the gut bacteria and the epithelia. To capture patient heterogeneity, we prioritized and pooled fecal material from 10 Crohn disease (CD), 10 ulcerative colitis (UC), and 10 healthy subjects. Prioritization of samples was based on our published gut microbial health index (PMID: 35197084), matching gender and age. Monolayered epithelial cells (Caco2 cells and patient-derived colonoids) were used for the co-culturing. Measurable outputs included cell viability, epithelial integrity, and secretion of CXCL1. Results Fecal samples were processed by separating the supernatant, heat-killing the bacteria, and rejoining the samples (Fig. 1A). 16S sequencing showed that bacterial composition and alpha diversity (Faith) were overall preserved after the heat-killing (Fig. 1B), as seen in the original samples. The gut microbial health index was higher among the control samples and pool, compared to the IBD samples (Fig. 1C), preserving the IBD pathogenic signals. Because previous studies indicated the enrichment of salivary bacteria in IBD feces, salivary samples were also processed for comparison. We confirmed that similar amounts of bacterial DNA (as a proxy of bacterial mass) were used for coculturing as indicated by qPCR of the 16S-V4 (Fig. 1D). Co-culturing the fecal and saliva pools with Caco-2 cells revealed a significant increase in CXCL1 proinflammatory chemokine secretion to the media in comparison to no-treatment (Fig. 2A). Moreover, the UC and CD pools significantly decreased epithelial integrity [transepithelial electrical resistance (TEER)], without affecting cellular viability (Fig. 2B-D). Finally, incubation of the fecal content with colon-derived organoids (from 2 controls and 1 UC) resulted in a substantial reduction of cell viability, which was more pronounced with fecal content derived from UC patients (Fig. 2E), and this effect was noted most with the UC fecal supernatants. Conclusion Using a novel co-culturing system, we demonstrated the effects of fecal contents from IBD and control subjects on CXCL1 secretion and epithelial integrity in Caco2 cells, and on colonoids viability. These models will be used to identify fecal factors and interventions relevant to IBD epithelial functions.

P1205 Features of the gut microbiota that associate with clinical outcomes of fecal microbiota transplantation in Ulcerative Colitis: a systematic review and meta-analysis

Abstract Background Evidence continues to accumulate highlighting the potential of fecal microbiota transplantation (FMT) to induce remission in patients with ulcerative colitis (UC). However, rational donor and recipient selection strategies and predictive biomarkers are needed to increase its efficacy. This systematic review provides a comprehensive evaluation of the current literature on microbial factors of FMT donors and UC recipients that relate to clinical outcomes. Methods The MEDLINE, Embase and Cochrane databases were systematically searched through April 2023 for relevant studies. The quality of studies and risk of bias was analyzed with Joanna Briggs tools and a compound critical appraisal-score. Additionally, species-level data from two randomized controlled trials (TURN and FOCUS) were re-analyzed from a compositional perspective. Results Out of 2983 citations identified, 47 met the inclusion criteria, of which 20 fulfilled quality appraisal. Higher clinical response rates were associated with higher bacterial alpha-diversity of stools of UC recipients at baseline and following FMT, and with higher FMT donor alpha-diversity. Engraftment of the donors’ microbiota was often reported but could not be clearly linked to clinical response, possibly because not every donor has an ideal microbiome. Taxa most frequently reported to be related to response included members of the Lachnospiraceae family (e.g., Eubacterium rectale, Blautia obeum) and Oscillospiraceae family (e.g., Faecalibacterium prausnitzii, Ruminococcus bromii) whereas members of the Proteobacteria and Fusobacteria phyla and Ruminococcus gnavus were reported to correlate to non-response. Low virome richness and low Caudovirales bacteriophages at baseline as well as a decrease of Candida levels following FMT, were associated with clinical response. Compositional analyses showed that a clinical response is associated with a shift away from a low diversity, Bacteroides2-enterotype-like composition towards one of high diversity either dominated by various butyrate producers, the Christensenellaceae-Methanobrevibacter trophic network or a high diversity composition with abundant but not excessive levels of Prevotella copri. Conclusion In this systematic review we found distinctive features of microbial profiles of both donors and UC recipients to relate to clinical response to FMT. The predictive value of microbial markers should be further explored in future clinical studies to move towards a personalized FMT approach and delineate ‘super-donor’ profiles.

Effects of carbon source addition in rearing water on sediment characteristics, growth and health of cultured marron (Cherax cainii)

Carbon sources are considered as critical input for the health and immunity of aquatic animals. The present study investigated the impact of different carbon sources on water quality parameters, carbon to nitrogen (C/N) ratio and microbial community in sediments, and health responses of marron (Cherax cainii) under laboratory conditions. Following one week of acclimation, 120 marron were randomly assigned to 12 experimental tanks. There were four treatments including one untreated control and three groups with carbon addition to maintain a C/N ratio of 12 maintained in culture water. Carbon supplementation groups included corn flour (CBC12), molasses (MBC12) and wheat flour (WBC12). At the end of the 60-day trial, MBC12 resulted in the highest sediment C/N ratio, followed by CBC12. Weight gain and specific growth rate were higher in MBC12, compared to control. The protease activity in marron hepatopancreas, total haemocyte count and lysozyme activity in haemolymph were highest in MBC12. Analysis of 16S rRNA sequence data of tank sediments revealed increased bacterial alpha diversity in MBC12 and WBC12. Proteobacteria was the most abundant phylum in MBC12 (88.6%), followed by control (82.4%) and CBC12 (72.8%). Sphingobium and Novosphingobium were the most abundant genera in control and MBC12 groups, respectively. Higher Aeromonas abundance in CBC12 and Flavobacterium in WBC12 were observed. Overall results indicated that MBC12 led to improved water quality, retaining high C/N ratio and enriched the bacterial populations in sediments resulting in improved growth and immune performance of marron.

Role of an arbuscular mycorrhizal fungus in vegetation restoration as indicated by bacterial diversity and microbial metabolic limitation in soil underlying moss biocrusts

Arbuscular mycorrhizal (AM) fungi contribute to the revegetation of degraded ecosystems such as coal mining areas and may indirectly affect the development of biological soil crusts (biocrusts). However, bacterial diversity and microbial nutrient cycling in the soil underlying biocrusts are seldom considered when assessing ecological restoration effects. Bacterial community composition was quantified and compared using 16S rRNA gene sequencing, metabolic limitation of microbes via extracellular enzymatic stoichiometry and their association with carbon use efficiency (CUE) in soil underlying moss biocrusts in vegetated areas inoculated with an AM fungus or uninoculated and in uninoculated unvegetated areas. The AM fungal inoculum significantly influenced bacterial community composition and diversity, extracellular enzyme activities and CUE in soil underlying moss biocrusts mainly by affecting soil nutrients. Correlation analysis revealed that Actinobacteria, Armatimonadetes, Bacteroidetes, Chlorobi, Cyanobacteria, Saccharibacteria, and Verrucomicrobia were positively correlated with soil nutrients carbon (C), nitrogen (N) and phosphorus (P). A vector analysis of extracellular enzyme activity indicates that soil microbial communities underlying moss biocrusts were limited by P but microbial communities in areas inoculated with the AM fungus had the lowest relative P limitation. The alleviation of microbial P limitation increased the microbial CUE and bacterial phylum community and alpha diversity, leading to an increase in subsoil C content underlying moss biocrusts. This indicates that microbial communities in soil underlying moss biocrusts under in restoration areas containing the AM fungus were more stable under environmental stress, and the inclusion of AM fungal inoculation may be recommended as the preferred option for ecosystem restoration in arid and semi-arid coal mining areas.

An Analysis of the Gut Microbiota and Related Metabolites following PCSK9 Inhibition in Statin-Treated Patients with Elevated Levels of Lipoprotein(a).

Atherosclerotic cardiovascular disease (ASCVD) is a leading cause of global mortality, often associated with high blood levels of LDL cholesterol (LDL-c). Medications like statins and PCSK9 inhibitors, are used to manage LDL-c levels and reduce ASCVD risk. Recent findings connect the gut microbiota and its metabolites to ASCVD development. We showed that statins modulate the gut microbiota including the production of microbial metabolites involved in the regulation of cholesterol metabolism such as short chain fatty acids (SCFAs) and bile acids (BAs). Whether this pleiotropic effect of statins is associated with their antimicrobial properties or it is secondary to the modulation of cholesterol metabolism in the host is unknown. In this observational study, we evaluated whether alirocumab, a PCSK9 inhibitor administered subcutaneously, alters the stool-associated microbiota and the profiles of SCFAs and BAs. We used stool and plasma collected from patients enrolled in a single-sequence study using alirocumab. Microbial DNA was extracted from stool, and the bacterial component of the gut microbiota profiled following an amplicon sequencing strategy targeting the V3-V4 region of the 16S rRNA gene. Bile acids and SCFAs were profiled and quantified in stool and plasma using mass spectrometry. Treatment with alirocumab did not alter bacterial alpha (Shannon index, p = 0.74) or beta diversity (PERMANOVA, p = 0.89) in feces. Similarly, circulating levels of SCFAs (mean difference (95% confidence interval (CI)), 8.12 [-7.15-23.36] µM, p = 0.25) and BAs (mean difference (95% CI), 0.04 [-0.11-0.19] log10(nmol mg-1 feces), p = 0.56) were equivalent regardless of PCSK9 inhibition. Alirocumab therapy was associated with increased concentration of BAs in feces (mean difference (95% CI), 0.20 [0.05-0.34] log10(nmol mg-1 feces), p = 0.01). In statin-treated patients, the use of alirocumab to inhibit PCSK9 leads to elevated levels of fecal BAs without altering the bacterial population of the gut microbiota. The association of alirocumab with increased fecal BA concentration suggests an additional mechanism for the cholesterol-lowering effect of PCSK9 inhibition.

Eimeria infections of plateau pika altered the patterns of temporal alterations in gut bacterial communities.

Intestinal parasites, such as Eimeria, are common among plateau pika (Ochotona curzoniae). The gut microbiome is an essential driver of the host response to gastrointestinal parasites. However, the effects of intestinal protozoal parasites on the temporal variations in the gut microbiome and behavioral and physiological activities remain unknown. Our study conducted treatments involving experimental feeding of pika with Eimeria oocysts or anticoccidia under laboratory conditions to focus on the parasite-associated alterations in gut bacterial communities, host behavioral activity, physiology, and host-bacteria relationships. The results showed insignificant differences in bacterial community structures among treatments on the basis of Bray-Curtis distance metrics, whereas the patterns of temporal alterations in the bacterial communities were changed by the treatments. Bacterial alpha diversities did not vary with the treatments, and experimental feeding with Eimeria slowed down the decrement rate of alpha diversity. Furthermore, few bacterial members were significantly changed by the treatments-only the genus Ruminococcus and the species Ruminococcus flavefaciens, which were associated with energy metabolism. Experimental feeding with Eimeria modified the temporal variations in the bacterial members, including a lower loss rate of the relative abundance of the dominant families Muribaculaceae and Ruminococcaceae in the group with Eimeria experimental feeding. Moreover, a shifting energy trade-off was suggested by the parasite-induced increments in thyroid hormones (triiodothyronine and tetraiodothyronine) and decrements in exploration behavior in the group with Eimeria feeding. However, we did not detect specific connections between gut bacterial communities and pika behaviors and physiology in terms of energy trade-offs. Further in-depth research is needed to examine the role of Eimeria-modified differences in the gut bacteria of plateau pika.

Biotic interactions outweigh abiotic factors as drivers of bark microbial communities in Central European forests.

Bark surfaces are extensive areas within forest ecosystems, which provide an ideal habitat for microbial communities, through their longevity and seasonal stability. Here we provide a comprehensive account of the bark surface microbiome of living trees in Central European forests, and identify drivers of diversity and community composition. We examine algal, fungal, and bacterial communities and their interactions using metabarcoding on samples from over 750 trees collected in the Biodiversity Exploratories in northern, central, and southern Germany. We show that mutual biotic influence is more important than the abiotic environment with regard to community composition, whereas abiotic conditions and geography are more important for alpha diversity. Important abiotic factors are the relative humidity and light availability, which decrease the algal and bacterial alpha diversity but strongly increase fungal alpha diversity. In addition, temperature is important in shaping the microbial community, with higher temperature leading to homogeneous communities of dominant fungi, but high turnover in bacterial communities. Changes in the community dissimilarity of one organismal group occur in close relation to changes in the other two, suggesting that there are close interactions between the three major groups of the bark surface microbial communities, which may be linked to beneficial exchange. To understand the functioning of the forest microbiome as a whole, we need to further investigate the functionality of interactions within the bark surface microbiome and combine these results with findings from other forest habitats such as soil or canopy.

Climate and Environmental Variables Drive Stream Biofilm Bacterial and Fungal Diversity on Tropical Mountainsides.

High mountain freshwater systems are particularly sensitive to the impacts of global warming and relevant environmental changes. Microorganisms contribute substantially to biogeochemical processes, yet their distribution patterns and driving mechanism in alpine streams remain understudied. Here, we examined the bacterial and fungal community compositions in stream biofilm along the elevational gradient of 745-1874 m on Mt. Kilimanjaro and explored their alpha and beta diversity patterns and the underlying environmental drivers. We found that the species richness and evenness monotonically increased towards higher elevations for bacteria, while were non-significant for fungi. However, both bacterial and fungal communities showed consistent elevational distance-decay relationships, i.e., the dissimilarity of assemblage composition increased with greater elevational differences. Bacterial alpha diversity patterns were mainly affected by chemical variables such as total nitrogen and phosphorus, while fungi were affectedby physical variables such as riparian shading and stream width. Notably, climatic variables such as mean annual temperature strongly affected the elevational succession of bacterial and fungal community compositions. Our study is the first exploration of microbial biodiversity and their underlying driving mechanisms for stream ecosystems in tropical alpine regions. Our findings provide insights on the response patterns of tropical aquatic microbial community composition and diversity under climate change.

Effects of diets supplemented with bioactive peptides on nutrient digestibility, immune cell responsiveness, and fecal characteristics, microbiota, and metabolites of adult cats.

Bioactive peptides (BP) are recognized for their ability to function as antioxidants and maintain lipid stability. They may have positive health effects, including antihypertensive, anti-inflammatory, antimicrobial, osteoprotective, gut health, and immunomodulatory properties, but are poorly tested in cats. Our primary objective was to determine the apparent total tract digestibility (ATTD) of BP-containing kibble diets and assess how the fecal characteristics, metabolites, and microbiota were affected in adult cats. Our secondary objective was to test whether BP could impact blood oxidative stress markers and cytokine concentrations following transport stress. Twelve adult cats (4.83±0.37 yr; 4.76±0.14kg) were used in a replicated 4×4 Latin square design to test four extruded kibble diets: Control (no BP), Chicken (4% chicken BP), Marine1 (2% marine BP), and Marine2 (4% marine BP). Each experimental period lasted 28 d, with a 20-d adaptation phase, 5 d for fecal collection, 2 d for blood collection, and 1 d for transport stress testing (driven in vehicle in individual carriers for 45min). Salivary cortisol and blood oxidative stress markers and cytokines were measured after transport. Fecal microbiota data were evaluated using 16S rRNA gene amplicon sequencing and QIIME2. All other data were analyzed using the Mixed Models procedure of SAS, with P<0.05 being considered significant and P<0.10 considered trends. No differences were observed in animal health outcomes, with all cats remaining healthy and serum metabolites remaining within reference ranges. Cats fed the Marine2 diet had higher (P<0.05) ATTD of dry matter (84.5% vs. 80.9%) and organic matter (88.3% vs. 85.8%) than those fed the control diet. The ATTD of protein and energy tended to be higher (P<0.10) for cats fed the Marine2 diet. Fecal characteristics, metabolites, and bacterial alpha and beta diversity measures were not affected by treatment. However, the relative abundances of six bacterial genera were different (P<0.05) and two bacterial genera tended to be different (P<0.10) across treatments. Treatment did not alter salivary cortisol, blood oxidative stress markers, or blood cytokines after transport stress. Our data suggest that BP inclusion may increase nutrient digestibility and modify fecal microbiota and immune measures. More testing is required, however, to determine whether BP may provide additional benefits to cats.

Effects of a veterinary gastrointestinal diet on fecal characteristics, metabolites, and microbiota concentrations of adult cats treated with metronidazole.

Antibiotics are used to treat gastrointestinal diseases or infections but are known to negatively affect stool quality and gut microbiota in cats and dogs. Therefore, identifying dietary strategies that may aid in antibiotic recovery is of interest. The objective of this study was to determine how a veterinary gastrointestinal diet affected the fecal characteristics, microbiota, and metabolite and bile acid (BA) concentrations of cats recovering from metronidazole administration. Twenty-four healthy adult cats were used in an 8-wk completely randomized design study. During a 2-wk baseline, all cats consumed a leading grocery brand diet (GBD). Over the next 2wk, cats consumed GBD and received metronidazole (20mg/kg body weight twice daily). At week 4, cats were randomly allotted to one of 2 treatments [GBD; BLUE Natural Veterinary Diet GI Gastrointestinal Support (BB)] and fed for 4wk. Fecal scores were recorded daily and fresh fecal samples were collected at weeks 2, 4, 5, 6, 7, and 8 for measurement of pH, dry matter (DM) %, metabolites, and microbiota. Microbiota was analyzed by 16S rRNA gene sequencing and qPCR, which was used to calculate dysbiosis index. Data were analyzed as repeated measures using the Mixed Models procedure of SAS 9.4, testing for effects of diet, time and diet*time. Metronidazole had dramatic effects on all outcomes, including increased fecal scores (looser stools), reduced fecal pH and DM%, reduced fecal short-chain fatty acid, branched-chain fatty acid, ammonia, phenol, and indole concentrations, and altered fecal BA concentrations (increased primary BA; reduced secondary BA). Metronidazole reduced fecal bacterial alpha diversity, increased dysbiosis index, and altered the relative abundance of 78 bacterial genera. Fecal outcomes partially recovered over the next 4wk, with some being impacted by diet. Fecal acetate concentrations were higher after metronidazole in cats fed BB. Dysbiosis index and alpha diversity measures slowly recovered over 4wk, without diet differences. Recovery of 16 bacterial genera was impacted by diet. Fecal BA profiles demonstrated a prolonged impairment of primary to secondary BA conversion, with cholic acid being lower after metronidazole in cats fed BB. In conclusion, our data demonstrate that metronidazole is a powerful antibiotic that has long-lasting effects on the fecal microbiota and metabolites of cats. Outcome variables slowly recovered over time, but a gastrointestinal diet may aid in recovery.

Effects of a novel dental chew on oral health outcomes, halitosis, and microbiota of adult dogs.

Halitosis in dogs is an initial indication of periodontitis, highlighting its significance as a vital marker for underlying problems. Moreover, the oral microbial population has a significant influence on periodontal disease. Measuring the oral microbiota may be used in addition to breath odor, dental plaque, and gingivitis scoring to assess the impact of dental chews on oral health. In this study, we aimed to determine the differences in breath odor, oral health outcomes, and oral microbiota of adult dogs consuming a novel dental chew compared with control dogs consuming only a diet. Twelve healthy adult female beagle dogs were used in a crossover design study. Treatments (n = 12/group) included: diet only (control) or the diet + a novel dental chew. Each day, one chew was provided 4h after mealtime. On days 1, 7, 14, 21, and 27, breath samples were analyzed for total volatile sulfur compound concentrations using a halimeter. On day 0 of each period, teeth were cleaned by a veterinary dentist blinded to treatments. Teeth were scored for plaque, calculus, and gingivitis by the same veterinary dentist on day 28 of each period. After scoring, subgingival and supragingival plaque samples were collected for microbiota analysis using Illumina MiSeq. All data were analyzed using SAS (version 9.4) using the Mixed Models procedure, with P < 0.05 being significant. Overall, the dental chews were well accepted. Dogs consuming the dental chews had lower calculus coverage, thickness, and scores, lower gingivitis scores, and less pocket bleeding than control dogs. Breath volatile sulfur compounds were lower in dogs consuming the dental chews. Bacterial alpha-diversity analysis demonstrated that control dogs had higher bacterial richness than dogs fed dental chews. Bacterial beta-diversity analysis demonstrated that samples clustered based on treatment. In subgingival and supragingival plaque, control dogs had higher relative abundances of potentially pathogenic bacteria (Pelistega, Desulfovibrio, Desulfomicrobium, Fretibacterium, Helcococcus, and Treponema) and lower relative abundances of genera associated with oral health (Neisseria, Actinomyces, and Corynebacterium). Our results suggest that the dental chew tested in this study may aid in reducing periodontal disease risk in dogs by beneficially shifting the microbiota population and inhabiting plaque buildup.

The effects of fermented vegetables on the gut microbiota for prevention of cardiovascular disease.

This study investigated the impact of regular consumption of fermented vegetables (FVs) on inflammation and the composition of the gut microbiota in adults at increased risk for cardiovascular disease. Eighty-seven adults ages 35-64 were randomized into an FV group, who consumed 100g FVs daily at least five times per week for eight weeks, or a usual diet (UD) group. Blood and stool samples were obtained before and after the intervention. Dependent samples t tests and adjusted linear models were used for within- and between-group comparisons. The mean age and body mass index of participants were 45years and 30kg/m2, and 80% were female. Bloating or gas was the most common side effect reported (19.3% FV group vs. 9.4% UD group). There were no changes in C-reactive protein, oxidized low-density lipoprotein-receptor 1, angiopoietin-like protein 4, trimethylamine oxide, and lipopolysaccharide-binding protein or bacterial alpha diversity between groups. Our findings indicate that consuming 100g of FVs for at least five days per week for eight weeks does not change inflammatory biomarkers or microbial alpha diversity as measured by the Shannon index. It is possible that higher doses of FVs are necessary to elicit a significant response by gut bacteria.

Bacterial Diversity in Placentas from Complicated Pregnancies Using 16s rRNA Gene Sequencing

Introduction: The ‘sterile womb paradigm’ is currently under debate and the advent of next generation 16S rRNA gene sequencing is driving the characterization of microbes associated with the amniotic cavity during pregnancy. Objective: To characterize the bacterial diversity in placentas from preterm and term births using next generation 16S rRNA gene sequencing in association with adverse pregnancy outcomes and histopathology studies. Methods: In this prospective study, placentas were collected consecutively from patients attending a public tertiary referral hospital in South Africa, delivering preterm (n=42; 28-34 weeks gestational age) and term (n=20; &gt;37 weeks gestational age). Placentas underwent histopathology tests and next generation 16S rRNA gene sequencing. Results: Analysis of microbial diversity in the placenta showed a significantly higher alpha diversity in term placentas compared to preterm placentas (P=0.000075), in placentas with acute chorioamnionitis compared to placentas without acute chorioamnionitis (P=0.0061), between HIV negative term births and both HIV negative and HIV positive preterm births (P=0.0118 and P=0.0008), respectively. Beta diversity was significantly different between preterm and term births (unweighted UniFrac distance, P=0.003996; Jaccard distance, P=0.03696) and Escherichia/Shigella, Shuttleworthia, Anaeroglobus and Megasphaera were differentially expressed. Conclusion: This is the first South African study to characterize the bacterial diversity in placentas from complicated pregnancies using next generation 16S rRNA gene sequencing in conjunction with full placental histology. Microbial diversity differs between preterm and term placentas where HIV may act as a cofactor associated with decreased bacterial alpha diversity in placentas from preterm birth.

The effects of dairy on the gut microbiome and symptoms in gastrointestinal disease cohorts: a systematic review.

Bovine dairy foods provide several essential nutrients. Fermented bovine dairy foods contain additional compounds, increasing their potential to benefit gastrointestinal health. This review explores the effects of dairy consumption on the gut microbiome and symptoms in gastrointestinal disease cohorts. Human subjects with common gastrointestinal diseases (functional gastrointestinal disorders and inflammatory bowel disease) or associated symptoms, and equivalent animal models were included. A systematic literature search was performed using PubMed, Embase and Web of Science. The search yielded 3014 studies in total, with 26 meeting inclusion criteria, including 15 human studies (1550 participants) and 11 animal studies (627 subjects). All test foods were fermented bovine dairy products, primarily fermented milk and yogurt. Six studies reported increases in gastrointestinal bacterial alpha diversity, with nine studies reporting increases in relative Lactobacillus and Bifidobacterium abundance. Six studies reported increases in beneficial short-chain fatty acids, while three reported decreases. Gastrointestinal symptoms, specifically gut comfort and defecation frequency, improved in 14 human studies. Five animal studies demonstrated reduced colonic damage and improved healing. This review shows fermented bovine dairy consumption may improve gut microbial characteristics and gastrointestinal symptoms in gastrointestinal disease cohorts. Further human intervention studies are needed, expanding test foods and capturing non-self-reported gastrointestinal measures.

Soil bacterial community composition is altered more by soil nutrient availability than pH following long-term nutrient addition in a temperate steppe.

Although aboveground biodiversity has been extensively studied, the impact of nutrient enrichment on soil microbial populations remains unclear. Soil microorganisms serve as important indicators in shaping soil nutrient cycling processes and are typically sensitive to nutrient additions. For this, we employed a factorial combination design to examine the impact of nutrient additions on the composition and function of soil bacteria in a temperate steppe. Nitrogen addition promoted the growth of copiotrophic bacteria (Proteobacteria, Firmicutes, and Bacteroidota) but inhibited the growth of oligotrophic bacteria (Acidobacteria, Chloroflexi, and Verrucomicrobiota). Phosphorus addition alleviated phosphorus deficiency, resulting in a decrease in the abundance of phoD-harboring bacteria (Actinobacteria and Proteobacteria). Significant enhancement of soil bacterial alpha diversity was observed only in treatments with added phosphorus. Changes in NO3 --N, NH4 +-N, available phosphorus, and dissolved organic carbon resulting from nutrient addition may have a greater impact on microbial community structure than changes in soil pH caused by nitrogen addition. Moreover, nutrient addition may indirectly impact microbial ecological function by altering nutrient availability in the soil. In conclusion, our study suggests that soil nutrient availability, particularly available phosphorus, affects soil bacterial communities and potentially regulates the biogeochemical cycles of soil ecosystems.

Differential Responses of Bacterial Communities in Rhizosphere and Bulk Soils of Cotton to Long-Term Amelioration Practices Based on Freezing Saline Water Irrigation and Plastic Mulching in a Coastal Saline Soil

Soil amelioration in coastal saline areas plays an important role in alleviating land resource shortages, improving regional ecological environments, ensuring food security, and promoting economic development. Plastic mulching (M) and the combination of freezing saline water irrigation and plastic mulching (WIM) are successful amelioration practices that dramatically reduce the salinity of surface soil and facilitate plant growth in coastal saline soil. However, the bacterial responses that are closely related to these amelioration practices in coastal saline soil remain poorly understood. In this study, bacterial richness and diversity, community composition, and potential ecological functions in the rhizosphere and bulk soils of cotton in M and WIM treatments, along with a control treatment, were investigated using high-throughput sequencing in a coastal saline field. The results showed that both the M and WIM treatments increased bacterial richness and alpha diversity, which were in general significantly higher in bulk soil than in rhizosphere soil. Non-metric multidimensional scaling and the Bray–Curtis dissimilarity analysis revealed that the bacterial community in rhizosphere soil was assembled far from those in the control and bulk soils and behaved more specifically in rhizosphere soil than in bulk soil. The relative abundances of most of the dominant phyla showed opposite trends of variation in bulk and rhizosphere soils compared to those in control soil in both M and WIM treatments; in particular, the specific bacterial groups of Proteobacteria and Actinobacteria decreased in bulk soil but significantly increased in rhizosphere soil. Functional groups of chemoheterotrophy, aerobic chemoheterotrophy, and nitrate reduction were predominant in rhizosphere rather than bulk soil, according to the Functional Annotation of Prokaryotic Taxa. These findings improve the understanding of the mechanism of bacterial responses to amelioration practices M and WIM in coastal saline soils and provide valuable information for the development of amelioration techniques based on agricultural practices and soil microbiome to enhance plants’ adaptability to saline soil in the future.

Soil microbial community structure, function and network along a mangrove forest restoration chronosequence

Mangrove forests have high ecological, social and economic values, but due to environmental changes and human activities, natural mangrove forests have experienced serious degradations and reductions in distribution area worldwide. In the coastal zones of southern China, an introduced mangrove species, Sonneratia apetala, has been extensively used for mangrove restoration because of its rapid growth and strong environmental adaptability. However, little is known about how soil microorganisms vary with the restoration stages of the afforested mangrove forests. Here, we examined the changes in soil physicochemical properties and microbial biomass, community structure and function, and network in three afforested S. apetala forests with restoration time of 7, 12, and 18 years and compared them with a bare flat and a 60-year-old natural Kandelia obovata forest in a mangrove nature reserve. Our results showed that the contents of soil salinity, organic carbon, total nitrogen, ammonium nitrogen, and microbial biomass increased, while soil pH and bacterial alpha diversity decreased with afforestation age. Soil microbial community structure was significantly affected by soil salinity, organic carbon, pH, total nitrogen, ammonium nitrogen, available phosphorus, and available kalium, and susceptibility to environmental factors was more pronounced in bacterial than fungal community structure. The relative abundances of aerobic chemoheterotrophy were significantly higher in 12- and 18-year-old S. apetala than in K. obovata forest, while that of sulfate-reducing bacteria showed a decreasing trend with afforestation age. The abundance of dung saprotroph was significantly higher in 12- and 18-year-old S. apetala forests than in the natural forest. With the increasing afforestation age, the modularity of microbial networks increased, while stability and robustness decreased. Our results suggest that planting S. apetala contributes to improving soil fertility and microbial biomass but may make soil microbial networks more vulnerable.

Biochar Mitigates the Negative Effects of Microplastics on Sugarcane Growth by Altering Soil Nutrients and Microbial Community Structure and Function.

Microplastic pollution in sugarcane areas of China is severe, and reducing the ecological risks is critical. Biochar has been widely used in soil remediation. This study aims to explore the effects and mechanisms of microplastics combined with or without biochar on sugarcane biomass, soil biochemical properties in red soil through a potted experiment. The results show that, compared with control (CK), treatments with microplastics alone reduced the dry biomass of sugarcane, soil pH, and nitrogen (N) and phosphorus (P) contents by an average of 8.8%, 2.1%, 1.1%, and 2.0%, respectively. Interestingly, microplastics combined with biochar could alleviate the negative effects of microplastic accumulation on sugarcane growth and soil quality. There were significant differences in the bacterial community alpha diversity indices and compositions among different treatments. Compared with CK, treatments with microplastics alone obviously decreased the observed operational taxonomic units (OTUs) and the Chao1 and Shannon indices of soil total bacteria (16S rRNA gene-based bacteria) while increasing them in phoD-harboring bacteria. Microplastics combined with biochar treatments significantly increased the abundance of Subgroup_10 for the 16S rRNA gene and treatments with microplastics alone significantly increased the relative abundance of Streptomyces for the phoD gene compared to CK. Moreover, compared with microplastics alone, the treatments with microplastics combined with biochar increased the relative abundance of Subgroup_10, Bacillus, Pseudomonas in soil total bacteria, and Amycolatopsis and Bradyrhizobium in phoD-harboring bacteria, most of which can inhibit harmful bacteria and promote plant growth. Additionally, different treatments also changed the abundance of potential microbial functional genes. Compared to CK, other treatments increased the abundance of aerobic ammonia oxidation and denitrification but decreased the abundance of nitrate respiration and nitrogen respiration; meanwhile, these four functional genes involved in N cycling processes were obviously higher in treatments with microplastics combined with biochar than in treatments with microplastics alone. In conclusion, microplastics combined with biochar could alleviate the negative effects of microplastic accumulation on sugarcane biomass by altering soil nutrients and microbial community structure and function.

Effects of short-term drought, nitrogen application and their interactions on the composition and functional genes of soil microbial communities in alfalfa grassland on the Loess Plateau

Drought and nitrogen addition are important factors influencing soil microorganisms and changes in the soil environment. In the future, droughts will become more frequent, shorter, and more severe. However, little is known about the soil organic carbon components, enzyme activity, and composition, structure, and functional genes of soil microbial communities under short-term drought and nitrogen application conditions. In this study, we used metagenomics sequencing technology to explore the changes in the composition and functional genes of soil microbial communities under short-term drought, nitrogen application, and their interactions in the artificial grasslands of the Loess Plateau. The results indicated that (I) short-term drought, nitrogen application, and their interactions all increased the particulate organic carbon (POC) content. (II) Short-term drought increased the contents of soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN), as well as soil enzyme activity. (III) Short-term drought significantly increased the bacterial alpha diversity, whereas the interactions of short-term drought and nitrogen application enhanced the fungal alpha diversity. (IV) The interactions of short-term drought and nitrogen application inhibited Fusarium to prevent plant diseases. (V) Short-term drought enriched the relative abundance of genes related to carbon cycling and amino acid metabolism, while nitrogen application reduced genes related to carbon cycling but enriched genes related to glycan biosynthesis and metabolism. These results clearly showed that, short-term drought altered the composition and functional genes of soil microbial communities. Our research suggests that in the event of frequent short-term droughts in the future, nitrogen addition can be considered to maintain the diversity of soil microbial communities and sustain soil carbon and nitrogen cycling.