{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T10:15:25Z","timestamp":1791022525171,"version":"4.1.0"},"reference-count":50,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2022,8,27]],"date-time":"2022-08-27T00:00:00Z","timestamp":1661558400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"earmarked fund","award":["CARS36"],"award-info":[{"award-number":["CARS36"]}]},{"name":"earmarked fund","award":["Z191100004019023"],"award-info":[{"award-number":["Z191100004019023"]}]},{"name":"2115 Talent Development Program of China Agricultural University","award":["CARS36"],"award-info":[{"award-number":["CARS36"]}]},{"name":"2115 Talent Development Program of China Agricultural University","award":["Z191100004019023"],"award-info":[{"award-number":["Z191100004019023"]}]},{"name":"Beijing Key Research and Development Program","award":["CARS36"],"award-info":[{"award-number":["CARS36"]}]},{"name":"Beijing Key Research and Development Program","award":["Z191100004019023"],"award-info":[{"award-number":["Z191100004019023"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>This study aimed to investigate whether agricultural by-products with a high NDF content and small-particle-size substitute for forage could cause hindgut acidosis and dysbacteriosis in lactating dairy cows. We investigated the impact of soybean hull and beet pulp on the fecal fermentation, bacterial community, and digestibility of cows. Sixteen lactating Holstein cows were treated as follows (% of dry matter (DM)): amount of by-product added was 0 (control, CON), 1.67% (low by-products, LB), 3.33% (medium by-products, MB), and 5% (high by-products, HB). The results showed the fecal pH of cows to be 7.23\u20137.29, implying no hindgut acidosis. With increased inclusion of by-products in the diets, the proportion of fecal propionate; relative abundance of the phylum Bacteroidetes, the family Lachnospiraceae, and genera unclassified_f_Lachnospiraceae, Acetitomaculum, and Prevotella; and the DM and NDF digestibility of cows all increased linearly. Meanwhile, the fecal genera Turicibacter and Clostridium_sensu_stricto_1 decreased linearly. By-products promoted the abundance of fecal bacteria genes related to energy metabolism, glycolysis\/gluconeogenesis, and propanoate metabolism; and correlations between fecal short chain fatty acids, digestibility, and the bacteria genera were seen. Overall, our study suggested that adding 5% by-products could be a viable dietary formulation strategy that promotes digestibility and makes positive changes in hindgut fermentation and bacteria.<\/jats:p>","DOI":"10.3390\/microorganisms10091731","type":"journal-article","created":{"date-parts":[[2022,8,29]],"date-time":"2022-08-29T03:34:56Z","timestamp":1661744096000},"page":"1731","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Possibility of Using By-Products with High NDF Content to Alter the Fecal Short Chain Fatty Acid Profiles, Bacterial Community, and Digestibility of Lactating Dairy Cows"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8606-9698","authenticated-orcid":false,"given":"Jiaying","family":"Lyu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk, Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhantao","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk, Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5828-3723","authenticated-orcid":false,"given":"Erdan","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk, Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gaokun","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk, Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yajing","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk, Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk, Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengli","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk, Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,8,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.3168\/jds.S0022-0302(02)74179-9","article-title":"Effect of Concentrate Level and Feeding Management on Chewing Activities, Saliva Production, and Ruminal pH of Lactating Dairy Cows","volume":"85","author":"Maekawa","year":"2002","journal-title":"J. Dairy Sci."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.3168\/jds.2011-4421","article-title":"Invited review: Role of physically effective fiber and estimation of dietary fiber adequacy in high-producing dairy cattle","volume":"95","author":"Zebeli","year":"2012","journal-title":"J. Dairy Sci."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.anifeedsci.2009.09.012","article-title":"Effects of feeding cows in early lactation with soy hulls as partial forage replacement on heat production, retained energy and performance","volume":"155","author":"Miron","year":"2010","journal-title":"Anim. Feed Sci. Technol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"3376","DOI":"10.3168\/jds.S0022-0302(85)81251-0","article-title":"Symposium: Energy nutrition and metabolism of the lactation cow. Digestion and absorption of energy substrates in the lactating cow","volume":"68","author":"Sutton","year":"1985","journal-title":"J. Dairy Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1120","DOI":"10.2527\/jas.2010-3460","article-title":"Ruminant Nutrition Symposium: Productivity, digestion, and health responses to hindgut acidosis in ruminants","volume":"89","author":"Gressley","year":"2011","journal-title":"J. Anim. Sci."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1007\/s00284-015-0931-6","article-title":"A Meta-analysis of Bacterial Diversity in the Feces of Cattle","volume":"72","author":"Kim","year":"2016","journal-title":"Curr. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"s399","DOI":"10.1017\/S1751731118001921","article-title":"Review: Enhancing gastrointestinal health in dairy cows","volume":"12","author":"Plaizier","year":"2018","journal-title":"Animal"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2662","DOI":"10.3168\/jds.2011-5080","article-title":"Meta-analysis reveals threshold level of rapidly fermentable dietary concentrate that triggers systemic inflammation in cattle","volume":"95","author":"Zebeli","year":"2012","journal-title":"J. Dairy Sci."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.anifeedsci.2011.12.004","article-title":"Subacute ruminal acidosis (SARA), endotoxins and health consequences","volume":"172","author":"Plaizier","year":"2012","journal-title":"Anim. Feed Sci. Technol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"683","DOI":"10.2527\/jas.2013-6841","article-title":"Investigation of bacterial diversity in the feces of cattle fed different diets","volume":"92","author":"Kim","year":"2014","journal-title":"J. Anim. Sci."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"5019","DOI":"10.3168\/jds.2018-15704","article-title":"Graded replacement of corn grain with molassed sugar beet pulp modulates the fecal microbial community and hindgut fermentation profile in lactating dairy cows","volume":"102","author":"Petri","year":"2019","journal-title":"J. Dairy Sci."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"3977","DOI":"10.2527\/jas.2010-2900","article-title":"Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing","volume":"88","author":"Callaway","year":"2010","journal-title":"J. Anim. Sci."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"9551","DOI":"10.3168\/jds.2017-12765","article-title":"Physically adjusted neutral detergent fiber system for lactating dairy cow rations. I: Deriving equations that identify factors that influence effectiveness of fiber","volume":"100","author":"White","year":"2017","journal-title":"J. Dairy Sci."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"5397","DOI":"10.3168\/jds.2010-3411","article-title":"Effects of corn silage hybrids and dietary nonforage fiber sources on feed intake, digestibility, ruminal fermentation, and productive performance of lactating Holstein dairy cows","volume":"93","author":"Holt","year":"2010","journal-title":"J. Dairy Sci."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1111\/jpn.12094","article-title":"Effects of inclusion of graded amounts of soya bean hulls on feed intake, chewing activity and nutrient digestibility in dairy cows","volume":"98","author":"Mohammadzadeh","year":"2014","journal-title":"J. Anim. Physiol. Anim. Nutr."},{"key":"ref_16","unstructured":"NRC (2001). Nutrient Requirements of Dairy Cows, The National Research Council."},{"key":"ref_17","unstructured":"AOAC International (2005). Official Methods of Analysis, Association of Official Analytical Chemists. [16th ed.]."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"3583","DOI":"10.3168\/jds.S0022-0302(91)78551-2","article-title":"Methods for dietary fiber, neutral detergent fiber, and nonstarch polysaccharides in relation to animal nutrition","volume":"74","author":"Robertson","year":"1991","journal-title":"J. Dairy Sci."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Wang, E., Wang, J., Lv, J., Sun, X., Kong, F., Wang, S., Wang, Y., Yang, H., Cao, Z., and Li, S. (2021). Comparison of Ruminal Degradability, Indigestible Neutral Detergent Fiber, and Total-Tract Digestibility of Three Main Crop Straws with Alfalfa Hay and Corn Silage. Animals, 11.","DOI":"10.3390\/ani11113218"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"4475","DOI":"10.3168\/jds.2016-12266","article-title":"Effect of undigested neutral detergent fiber content of alfalfa hay on lactating dairy cows: Feeding behavior, fiber digestibility, and lactation performance","volume":"100","author":"Fustini","year":"2017","journal-title":"J. Dairy Sci."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ejsobi.2016.02.004","article-title":"Effect of biochar additions to soil on nitrogen leaching, microbial biomass and bacterial community structure","volume":"74","author":"Xu","year":"2016","journal-title":"Eur. J. Soil Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","article-title":"FLASH: Fast length adjustment of short reads to improve genome assemblies","volume":"27","author":"Magoc","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/nmeth.2604","article-title":"UPARSE: Highly accurate OTU sequences from microbial amplicon reads","volume":"10","author":"Edgar","year":"2013","journal-title":"Nat. Methods"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy","volume":"73","author":"Wang","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1038\/nbt.2676","article-title":"Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences","volume":"31","author":"Langille","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"ref_27","first-page":"145","article-title":"corrplot: Visualization of a correlation matrix","volume":"52","author":"Wei","year":"2013","journal-title":"Morb. Mortal. Wkly. Rep."},{"key":"ref_28","unstructured":"Lyu, J.Y. (2022). manuscript in preparation."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/j.tvjl.2007.12.016","article-title":"Subacute ruminal acidosis in dairy cows: The physiological causes, incidence and consequences","volume":"176","author":"Plaizier","year":"2008","journal-title":"Vet. J."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/j.anaerobe.2013.02.005","article-title":"Grain-rich diets differently alter ruminal and colonic abundance of microbial populations and lipopolysaccharide in goats","volume":"20","author":"Klevenhusen","year":"2013","journal-title":"Anaerobe"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"8020","DOI":"10.3168\/jds.2019-18036","article-title":"Evaluation of fecal fermentation profile and bacterial community in organically fed dairy cows consuming forage-rich diets with different particle sizes","volume":"103","author":"Haselmann","year":"2020","journal-title":"J. Dairy Sci."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"13","DOI":"10.2527\/af.2016-0018","article-title":"Effects of grain feeding on microbiota in the digestive tract of cattle","volume":"6","author":"Khafipour","year":"2016","journal-title":"Anim. Front."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2765","DOI":"10.3168\/jds.2016-11994","article-title":"Differential effects of monensin and a blend of essential oils on rumen microbiota composition of transition dairy cows","volume":"100","author":"Scharen","year":"2017","journal-title":"J. Dairy Sci."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2206","DOI":"10.3389\/fmicb.2017.02206","article-title":"Effect of Dietary Forage to Concentrate Ratios on Dynamic Profile Changes and Interactions of Ruminal Microbiota and Metabolites in Holstein Heifers","volume":"8","author":"Zhang","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2242","DOI":"10.3168\/jds.2021-21025","article-title":"Effects of lactic acid-producing bacteria as direct-fed microbials on the ruminal microbiome","volume":"105","author":"Monteiro","year":"2022","journal-title":"J. Dairy Sci."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"8847","DOI":"10.3168\/jds.2016-11029","article-title":"Shredded beet pulp substituted for corn silage in diets fed to dairy cows under ambient heat stress: Feed intake, total-tract digestibility, plasma metabolites, and milk production","volume":"99","author":"Naderi","year":"2016","journal-title":"J. Dairy Sci."},{"key":"ref_37","first-page":"2467","article-title":"Compositional mixed modeling of methane emissions and ruminal volatile fatty acids from individual cattle and multiple experiments","volume":"95","author":"Rooke","year":"2017","journal-title":"J. Anim. Sci."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.livsci.2013.12.034","article-title":"Effects of isovalerate supplementation on microbial status and rumen enzyme profile in steers fed on corn stover based diet","volume":"161","author":"Liu","year":"2014","journal-title":"Livest. Sci."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1007\/s00248-017-0940-z","article-title":"Changes in Microbiota in Rumen Digesta and Feces Due to a Grain-Based Subacute Ruminal Acidosis (SARA) Challenge","volume":"74","author":"Plaizier","year":"2017","journal-title":"Microb. Ecol."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Wang, K., Zhang, H., Hu, L., Zhang, G., Lu, H., Luo, H., Zhao, S., Zhu, H., and Wang, Y. (2022). Characterization of the Microbial Communities along the Gastrointestinal Tract in Crossbred Cattle. Animals, 12.","DOI":"10.3390\/ani12070825"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.3168\/jds.2016-11680","article-title":"Source of supplemental dietary copper, zinc, and manganese affects fecal microbial relative abundance in lactating dairy cows","volume":"100","author":"Faulkner","year":"2017","journal-title":"J. Dairy Sci."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"780354","DOI":"10.3389\/fcimb.2022.780354","article-title":"Gut Dysbiosis in Ocular Mucous Membrane Pemphigoid","volume":"12","author":"Low","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.aninu.2021.06.013","article-title":"Different dietary protein sources influence growth performance, antioxidant capacity, immunity, fecal microbiota and metabolites in weaned piglets","volume":"8","author":"Zhang","year":"2022","journal-title":"Anim. Nutr."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"5489","DOI":"10.1128\/AEM.02220-08","article-title":"Alteration of the ileal microbiota of weanling piglets by the growth-promoting antibiotic chlortetracycline","volume":"75","author":"Rettedal","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1007\/s00484-019-01812-z","article-title":"Effect of different seasons (spring vs summer) on the microbiota diversity in the feces of dairy cows","volume":"64","author":"Li","year":"2020","journal-title":"Int. J. Biometeorol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"9668","DOI":"10.3168\/jds.2016-11398","article-title":"Characterization and comparison of the temporal dynamics of ruminal bacterial microbiota colonizing rice straw and alfalfa hay within ruminants","volume":"99","author":"Liu","year":"2016","journal-title":"J. Dairy Sci."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"3026","DOI":"10.1007\/s10620-020-06500-2","article-title":"Analysis of Gut Microbiome and Metabolite Characteristics in Patients with Slow Transit Constipation","volume":"66","author":"Tian","year":"2021","journal-title":"Dig. Dis. Sci."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"711359","DOI":"10.3389\/fmicb.2021.711359","article-title":"Circulating Levels of the Short-Chain Fatty Acid Acetate Mediate the Effect of the Gut Microbiome on Visceral Fat","volume":"12","author":"Nogal","year":"2021","journal-title":"Front. Microbiol"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1868","DOI":"10.1111\/jam.14873","article-title":"Effect of different glucogenic to lipogenic nutrient ratios on rumen fermentation and bacterial community in vitro","volume":"130","author":"Hua","year":"2021","journal-title":"J. Appl. Microbiol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"41403","DOI":"10.1038\/srep41403","article-title":"Characterization of faecal microbial communities of dairy cows fed diets containing ensiled Moringa oleifera fodder","volume":"7","author":"Sun","year":"2017","journal-title":"Sci. Rep."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/9\/1731\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:16:29Z","timestamp":1760141789000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/9\/1731"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,8,27]]},"references-count":50,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2022,9]]}},"alternative-id":["microorganisms10091731"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms10091731","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,8,27]]}}}